Abstract: Kuqa depression lies at the northern margin of Tarim basin, nearby the southern Tianshan Mountain. The Palaeogene Suweiyi Formation was formed during foreland basin developing phase and thick fluvial-delta and lacustrine sediments were deposited. The unique location of Kuqa depression and the large range successive outcrops of Suweiyi Formation provide favorable room to carry out the high-resolution sequence stratigraphic study and the major controlling factors discussion. Based on the relative distinguishable flooding surface, the Suweiyi Formation is classified into ten 4th order sequences and a number of 5th order sequences or parasequences. The 4th order sequence consists of incised valley fill, delta front mouth bar, prodelta, subaqueous distributary channel, evaporite salt lake and lacustrine deposits. The incised valley sandstone, delta front mouth bar sandstone and the subaqueous distributary channel sandstone of the 4th order sequence Pss1, Pss6, Pss3, Pss5 and Pss8 comprise main reservoir beds. The characteristics of 4th order sequences and the stacking patterns of parasequences indicate that under the tectonic subsidence background, the interplay of climate, lake level fluctuation and depositional supply controlled the development of the high order sequences. The climate and the depositional supply were the crucial factors. The aridity and the humidity effected the fluctuation of lake level and controlled the basin filling and sequence development. The difference of depositional supply of near thrust belt and far thrust belt made the depositional filling and stacking patterns of parasequences different.