There is a significant change of the basin-mountain mechanism on the southwestern margin of Tarim basin, and the present tectonic pattern take shape during late Miocene-early Pliocene. Analyzed the sediment lithology and heavy mineral assemblages of the Miocene -Pliocene in the Qibei 3 well, this paper has established the variational rules heavy minerals along stratigraphic profile in the vertical direction. According to the variations of content and composition of heavy minerals, the stratigraphic profile of Qibei 3 well could be divided into three segments from bottom to up: the stable heavy mineral segment, the slightly unstable heavy mineral segment and the unstable heavy mineral segment. The analyzing results of heavy minerals show the erosion area of metamorphic rock constantly increased with the profile up in the source area, while the erosion area of acid igneous rock reduced. Combined with sedimentary characteristics, the relationship between tectonic events and sedimentary responses has been made, and following uplifting periods have been identified in the West Kunlun Orogen during late Miocene-early Pliocene: the stable period from the Anju’An formation to the lower of Pakabulake formation in the Miocene, the staged uplifting period during the mid-upper of Pakabulake formation, and the strongly uplifting period since the Atushi formation in the Pliocene.