The petrological characteristics and heavy mineral assembly of the Jurassic System in Kuqa Basin are consistent with the tectonic evolution, which is the major factor controlling the filling process of Kuqa Basin. Controlled by the source areas at the both sides of the Basin, the matrixes are dominated by sedimentary rock, high-grade metamorphic rock, acid magmatic rock, and the highest heavy mineral assemblage of zircon-garnet-magnetite in the content. According to heavy mineral indexes, the Jurassic strata can be classified into three rhythmic units of heavy mineral. The lower sequence contains abundant heavy minerals and relatively high content of detritus and its matrixes primarily came form the recycling orogen. The assemblage of "zircon-garnet-magnetite" indicates that the sedimentary area in the early evolution period of the basin is relatively near the provenance. The middle sequence is different from the lower sequence in the heavy mineral assemblage and has the different characteristics from that of source rock. The heavy mineral assemblage is "garnet-zircon" with the highest content of garnet and its main matrices are the high-grade metamorphic rock, acid magmatic rock and hydrothermal vein at the northeastern edge of the basin. The middle and upper sequences are characterized by the clast provenance, which is primarily from the recycling orogen at the northern edge of the basin and secondarily from the southern uplift. As a result of the two provenances, the strata with apparent changes of heavy mineral assemblage and index better coincides with the interfaces of the secondary strata sequences, which reflects the denudation history and the filling process of the orogen at the northern edge of the basin.