The eastern Kuqa depression is rich in oil and gas resources, and its structural deformation mechanism is closely related to the Southern Tianshan orogenic belt. Based on conjugate joints in outcrops and distribution of residual Cretaceous, the characteristics of the palaeo uplift and palaeo stress field property in the eastern Kuqa depression at late Cretaceous were analyzed. Conjugate joints analysis in the Tugerming, Kezilenuer, Kuqa river, Kapushaliang river, Jidike and western Kuqa river outcrops indicates that the compressive stress direction of eastern Kuqa depression was NNW-SSE at Cenozoic while NE-SW at Mesozoic. The recovery of prototype basin demonstrates that the sedimentary center of Kuqa depression was roughly along well Dabei 1-Tubei 2-Kela 2, and developed Qiulitage-Xinhe-Yaha-Tiergen palaeo uplift belt at Cretaceous, which leads to thick residual Cretaceous in the north and thin residual Cretaceous in the south. Under the background of regional uplift and denudation at late Cretaceous, the east of Kuqa depression lift and been denudated due to tectonic compression, which results in the thinning of residual Cretaceous, and therefore the residual Cretaceous is thick east and thin west. The Tugerming anticline in the eastern Kuqa depression was a longstanding inherited sedimentary palaeo uplift at Carboniferous-Triassic, and became a tectonic palaeo uplift by further uplift at late Cretaceous, which leads to further thinning of residual Cretaceous around the anticline. The long axis strikes of the Tugerming anticline and residual Cretaceous isolines around the anticline and Well Kubei 1 and Kuqa river outcrop are all NW-SE, which further confirms that the palaeo tectonic stress direction was NE-SW at late Cretaceous in the eastern Kuqa depression. The late Cretaceous uplift and tectonic stress field in the eastern Kuqa depression is primarily related to the regional uplift in the north margin of Tethys basin group caused by the hyperplasia and collision of geological terrain in the Tethys orogenic belt.