In 1939 Chinese Nationalist Soldiers took the mausoleum from its position at the 'Lord's Enclosure' (Mongolian: Edsen Khoroo) in Mongolia to protect it from Japanese troops. It was taken through Communist-held territory in Yan'an some 900 km (560 mi) on carts to safety at a Buddhist monastery, the Dongshan Dafo Dian, where it remained for ten years. In 1949, as Communist troops advanced, the Nationalist Soldiers moved it another 200 km (120 mi) farther west to the famous Tibetan monastery of Kumbum Monastery or Ta'er Shi near Xining, which soon fell under Communist control. In early 1954, Genghis Khan's bier and relics were returned to the Lord's Enclosure in Mongolia. By 1956 a new temple was erected there to house them. In 1968 during the Cultural Revolution, Red Guards destroyed almost everything of value. The "relics" were remade in the 1970s and a great marble statue of Genghis was completed in 1989.

During the communist period in Mongolia, Genghis was often described as a reactionary, and positive statements about him were avoided. In 1962, the erection of a monument at his birthplace and a conference held in commemoration of his 800th birthday led to criticism from the Soviet Union and the dismissal of secretary Tömör-Ochir of the ruling Mongolian People's Revolutionary Party Central Committee.

One theory suggests the name stems from a palatalised version of the Mongolian and Turkic word tenggis, meaning "ocean", "oceanic" or "wide-spreading". (Lake Baikal and ocean were called tenggis by the Mongols. However, it seems that if they had meant to call Genghis tenggis they could have said, and written, "Tenggis Khan", which they did not.) Zhèng (Chinese: 正) meaning "right", "just", or "true", would have received the Mongolian adjectival modifier -s, creating "Jenggis", which in medieval romanization would be written "Genghis". It is likely that the 13th century Mongolian pronunciation would have closely matched "Chinggis".

Genghis Khan is regarded as one of the prominent Leaders in Mongolia's history. He is responsible for the emergence of the Mongols as a political and ethnic identity because there was no unified identity between the tribes that had cultural similarity. He reinforced many Mongol traditions and provided stability and unity during a time of almost endemic warfare between tribes. He is also credited for introducing the traditional Mongolian script and creating the first written Mongolian code of law, the Ikh Zasag ("Great Administration"). Mongolian President Tsakhiagiin Elbegdorj has noted that the Ikh Zasag heavily punished corruption and bribery, and he considers Genghis Khan a Teacher for anti-corruption efforts who sought equal protection under the law for all citizens regardless of status or wealth. On the 850th anniversary of Genghis's birth, the President stated "Chinggis ... was a man who deeply realized that the justice begins and consolidates with the equality of law, and not with the distinctions between people. He was a man who knew that the good laws and rules lived longer than fancy palaces." In summary, Mongolians see him as the fundamental figure in the founding of the Mongol Empire and therefore the basis for Mongolia as a country.

In the early 1990s, the memory of Genghis Khan underwent a powerful revival, partly in reaction to its suppression during the Mongolian People's Republic period. Genghis Khan became one of the central figures of the national identity. He is considered positively by Mongolians for his role in uniting warring tribes. For Example, Mongolians often refer to their country as "Genghis Khan's Mongolia", to themselves as "Genghis Khan's children", and to Genghis Khan as the "father of the Mongols" especially among the younger generation. However, there is a chasm in the perception of his brutality. Mongolians maintain that the historical records written by non-Mongolians are unfairly biased against Genghis Khan and that his butchery is exaggerated, while his positive role is underrated.

On October 6, 2004, a joint Japanese-Mongolian archaeological dig uncovered what is believed to be Genghis Khan's palace in rural Mongolia, which raises the possibility of actually locating the ruler's long-lost burial site. Folklore says that a river was diverted over his grave to make it impossible to find (the same manner of burial as the Sumerian King Gilgamesh of Uruk and Atilla the Hun). Other tales state that his grave was stampeded over by many horses, and that trees were then planted over the site, and the permafrost also did its part in hiding the burial site.

In the Middle East, and particularly in Iran, Genghis Khan is almost universally condemned as a destructive and genocidal warlord who caused enormous destruction to the population of these areas. Steven R. Ward wrote that "Overall, the Mongol violence and depredations killed up to three-fourths of the population of the Iranian Plateau, possibly 10 to 15 million people. Some historians have estimated that Iran's population did not again reach its pre-Mongol levels until the mid-20th century."

As of 2012, Elbegdorj issued a decree establishing Genghis Khan's birthday as a national holiday on the first day of winter (according to the Mongolian lunar calendar).

In the early 13th century, the Khwarazmian dynasty was governed by Shah Ala ad-Din Muhammad. Genghis Khan saw the potential advantage in Khwarazmia as a commercial trading partner using the Silk Road, and he initially sent a 500-man caravan to establish official trade ties with the empire. However, Inalchuq, the governor of the Khwarazmian city of Otrar, attacked the caravan, claiming that the caravan contained spies and therefore was a conspiracy against Khwarazmia. The situation became further complicated because the governor later refused to make repayments for the looting of the caravans and hand over the perpetrators. Genghis Khan then sent a second group of three ambassadors (two Mongols and a Muslim) to meet the Shah himself, instead of the governor Inalchuq. The Shah had all the men shaved and the Muslim beheaded and sent his head back with the two remaining ambassadors. Outraged, Genghis Khan planned one of his largest invasion campaigns by organizing together around 100,000 Soldiers (10 tumens), his most capable generals and some of his sons. He left a commander and number of troops in China, designated his successors to be his family members and likely appointed Ögedei to be his immediate successor and then went out to Khwarazmia.