In September 1913 in Göttingen, Weyl married Friederike Bertha Helene Joseph (March 30, 1893 – September 5, 1948) who went by the name Helene (nickname "Hella"). Helene was a daughter of Dr. Bruno Joseph (December 13, 1861 – June 10, 1934), a physician who held the position of Sanitätsrat in Ribnitz-Damgarten, Germany. Helene was a Philosopher (she was a disciple of phenomenologist Edmund Husserl) and also a translator of Spanish literature into German and English (especially the works of Spanish Philosopher José Ortega y Gasset). It was through Helene's close connection with Husserl that Hermann became familiar with (and greatly influenced by) Husserl's thought. Hermann and Helene had two sons, Fritz Joachim Weyl (February 19, 1915 – July 20, 1977) and Michael Weyl (September 15, 1917 – March 19, 2011), both of whom were born in Zürich, Switzerland. Helene died in Princeton, New Jersey on September 5, 1948. A memorial Service in her honor was held in Princeton on September 9, 1948. Speakers at her memorial Service included her son Fritz Joachim Weyl and mathematicians Oswald Veblen and Richard Courant. In 1950 Hermann married sculptress Ellen Bär (née Lohnstein) (April 17, 1902 – July 14, 1988), who was the widow of professor Richard Josef Bär (September 11, 1892 – December 15, 1940) of Zürich.

After taking a teaching post for a few years, Weyl left Göttingen for Zürich to take the chair of mathematics at the ETH Zurich, where he was a colleague of Albert Einstein, who was working out the details of the theory of general relativity. Einstein had a lasting influence on Weyl, who became fascinated by mathematical physics. In 1921 Weyl met Erwin Schrödinger, a theoretical Physicist who at the time was a professor at the University of Zürich. They were to become close friends over time. Weyl had some sort of childless love affair with Erwin's wife Annemarie (Anny) Schrödinger (née Bertel) (December 31, 1896 – October 3, 1965), while at the same time Anny was helping raise an illegitimate daughter of Erwin's named Ruth Georgie Erica March, who was born in 1934 in Oxford, England.

From 1904 to 1908 he studied mathematics and physics in both Göttingen and Munich. His doctorate was awarded at the University of Göttingen under the supervision of David Hilbert whom he greatly admired.

In 1911 Weyl published Über die asymptotische Verteilung der Eigenwerte (On the asymptotic distribution of eigenvalues) in which he proved that the eigenvalues of the Laplacian in the compact domain are distributed according to the so-called Weyl law. In 1912 he suggested a new proof, based on variational principles. Weyl returned to this topic several times, considered elasticity system and formulated the Weyl conjecture. These works started an important domain—asymptotic distribution of eigenvalues—of modern analysis.

His overall approach in physics was based on the phenomenological philosophy of Edmund Husserl, specifically Husserl's 1913 Ideen zu einer reinen Phänomenologie und phänomenologischen Philosophie. Erstes Buch: Allgemeine Einführung in die reine Phänomenologie (Ideas of a Pure Phenomenology and Phenomenological Philosophy. First Book: General Introduction).

George Pólya and Weyl, during a mathematicians' gathering in Zürich (9 February 1918), made a bet concerning the Future direction of mathematics. Weyl predicted that in the subsequent 20 years, mathematicians would come to realize the total vagueness of notions such as real numbers, sets, and countability, and moreover, that asking about the truth or falsity of the least upper bound property of the real numbers was as meaningful as asking about truth of the basic assertions of Hegel on the philosophy of nature. Any answer to such a question would be unverifiable, unrelated to experience, and therefore senseless.

However, within a few years Weyl decided that Brouwer's intuitionism did put too great restrictions on mathematics, as critics had always said. The "Crisis" article had disturbed Weyl's formalist Teacher Hilbert, but later in the 1920s Weyl partially reconciled his position with that of Hilbert.

From 1923 to 1938, Weyl developed the theory of compact groups, in terms of matrix representations. In the compact Lie group case he proved a fundamental character formula.

After about 1928 Weyl had apparently decided that mathematical intuitionism was not compatible with his enthusiasm for the phenomenological philosophy of Husserl, as he had apparently earlier thought. In the last decades of his life Weyl emphasized mathematics as "symbolic construction" and moved to a position closer not only to Hilbert but to that of Ernst Cassirer. Weyl however rarely refers to Cassirer, and wrote only brief articles and passages articulating this position.

In 1929, Weyl proposed a fermion for use in a replacement theory for relativity. This fermion would be a massless quasiparticle and carry electric charge. An electron could be split into two Weyl fermions or formed from two Weyl fermions. Neutrinos were once thought to be Weyl fermions, but they are now known to have mass. Weyl fermions are sought after for electronics applications to solve some problems that electrons present. Such quasiparticles were discovered in 2015, in a form of crystals known as Weyl semimetals, a type of topological material.

These results are foundational in understanding the symmetry structure of quantum mechanics, which he put on a group-theoretic basis. This included spinors. Together with the mathematical formulation of quantum mechanics, in large measure due to John von Neumann, this gave the treatment familiar since about 1930. Non-compact groups and their representations, particularly the Heisenberg group, were also streamlined in that specific context, in his 1927 Weyl quantization, the best extant bridge between classical and quantum physics to date. From this time, and certainly much helped by Weyl's expositions, Lie groups and Lie algebras became a mainstream part both of pure mathematics and theoretical physics.

By 1949, Weyl was thoroughly disillusioned with the ultimate value of intuitionism, and wrote: "Mathematics with Brouwer gains its highest intuitive clarity. He succeeds in developing the beginnings of analysis in a natural manner, all the time preserving the contact with intuition much more closely than had been done before. It cannot be denied, however, that in advancing to higher and more general theories the inapplicability of the simple laws of classical logic eventually results in an almost unbearable awkwardness. And the Mathematician watches with pain the greater part of his towering edifice which he believed to be built of concrete blocks dissolve into mist before his eyes."

Hermann Weyl was cremated in Zurich on December 12, 1955. His cremains remained in private hands until 1999, at which time they were interred in an outdoor columbarium vault in the Princeton Cemetery (aka the Princeton Cemetery of Nassau Presbyterian Church), located at 29 Greenview Avenue, Princeton (Mercer County), New Jersey. The remains of Hermann's son Michael Weyl (1917–2011) are interred right next to Hermann's ashes in the same columbarium vault in the Princeton Cemetery.