The Tertiary Kuqa depression is a foreland basin generated by flexural subsidence resulting from the southward thrusting of the southern Tianshan Mountains. Tertiary basin fills of the depression can be classified into four tectonic sequences bounded by gentle angular unconformities. The sequences are composed of two parts, the lower transgressive and the upper progradational successions, which are separated by a regional maximum transgressive surface. The development of these sequences is attributed to the foreland tectonic process from flexural subsidence caused by thrust loading to rebounded uplift due to the erosion and stress release. The generation of the angular unconformities defining the tectonic sequences has been interpreted as the result of the rebounded uplift and the following thrusting. It has been found that there is a significant difference in depositional pattern between the northeastern and the northwestern margins. The relatively strong thrusting and mountain building occurring along the northwestern margin resulted in the development of thick-bedded alluvial fan and angular unconformities. The northeastern margin, in contract, lacks thick alluvial fan accumulation due to weak thrusting. This difference is likely related to the pre-existing east-west partition of the basin basement.