The main ancestors of the Uygurs were the Ouigour people who lived on the Mongolian Plateau during the Sui and Tang dynasties. Many different names were used in historical records to refer to this group of people.

Historically, to resist oppression and slavery by the Turks, the Ouigour people united with some of the Tiele tribes to form the Ouigour tribal alliance. In 744, the Tang court conferred a title on Kutlug Bilge Khagan, who united the Ouigour tribes. In 788, the then Ouigour ruler wrote to the Tang emperor, requesting to have their name changed to "Uighur".

After the Uighur Khanate was defeated by the Kyrgyz people in 840, some of the Uighurs moved inland to live with the Han people, and the rest were divided into three sub-groups. One of the sub-groups moved to the Turpan Basin and the present-day Jimsar region, where they founded the Uighur Kingdom of Gaochang. Another moved to the Hexi Corridor, where they merged with local ethnic groups to become what was later known as the Yugurs. The third sub-group moved to the west of Pamir, scattered in areas from Central Asia to Kashgar, and joined the Karluk and Yagma peoples in founding the Kara-Khanid Khanate. There they merged with the Han people in the Turpan Basin and the Yanqi, Qiuci, Khotan, Shule, and other peoples in the Tarim Basin to form the main body of the modern Uygur ethnic group.

In the Yuan and Ming dynasties, the various ethnic groups in Xinjiang further merged. The Mongols, especially those of the Chagatai Khanate, were fused with the Uighurs, adding fresh blood to the Uighur group. In 1934, Xinjiang issued a government order, stipulating that "维吾尔" would be the standard Chinese name for Uygurs, which for the first time expressed the accurate meaning of "Uygur": to maintain unity among the people.

The Ouigours endured slavery under the rule of the Turks. With support from Tang Dynasty troops, they rebelled against the Eastern Turkic Khaganate and defeated the Western Turkic Khaganate and the Second Turkic Khaganate. After the demise of the Western Turkic Khaganate, some Turkic-speaking tribes migrated westward. One of these tribes gradually settled down in Asia Minor, and integrated with local ethnic groups. The Uygurs are not descendants of the Turks.

Since the modern times, some Pan-Turkism advocates with ulterior motives have described all peoples of the Turkic language family as "the Turks" using the untenable argument that the Turkic-speaking tribe integrated with the ancestors of the Turkish people after migrating westward. A language family and an ethnic group are two essentially different concepts. In China, ethnic groups speaking Turkic languages include the Uygurs, Kazaks, Kirgiz, Uzbeks, Tatars, Yugurs, and Salars, each with its own history and unique culture. These peoples cannot be referred to as "Turks".