A group of alluvial fans formed in the early Paleogene represent marginal sedimentary facies at the foot of the South Tianshan Mountain, Kuqa Depression, Tarim Basin, Xinjiang province. Two types of fans occurred in the middle–late Paleogene Kumugeliemu and Suweiyi formations: one alluvial, and the other fan delta deposited in a lacustrine setting. Within the early Neogene Jidike Formation, coastal subaqueous fans developed, probably in a deeper water lacustrine setting. The three types of fans are stacked vertically in outcrop with the sequence in ascending order: bottom alluvial, middle fan-delta, and top subaqueous. The subaqueous is a typical coarse-fan deposit occurring in the glutinite member of the Jidike Formation in some wells. Laterally, from the foreland to the lacustrine settings, the distribution pattern of sedimentary facies represents the same three fan types sequentially. The spatial distribution of these fans was controlled by the Paleogene–Neogene Basin transformation, and evolution with different types of fans developed in the Kuqa Depression in response. In the Paleogene, the Kuqa Depression was a rift basin where an alluvial fan was deposited in the foreland setting, which, by early Neogene, became a foreland basin when the lake level changed. With any rise in lake level, fan-deltas migrated from lacustrine to foreland settings, whereas when the lake level fell, fan migration was reversed. In the early Neogene, with increasing slope and rising lake level, fans progressed and covered the previous fan-delta and lacustrine mudstone. Eventually, subaqueous fans developed, forming the present spatial configuration of these three fan types.