The Mesozoic- Cenozoic in the southern slope of Kuqa belong to the Kuqa continental petroleum system. Oil and gas mainly come from transverse migration of hydrocarbons generated by Triassic and Jurassic source rocks in the Kuqa Depression. In this paper, the characteristics of petroleum geochemical composition of Cretaceous and Paleogene discovered in the southern slope zone of Kuqa have been studied in detail by means of chromatography, chromatography- mass spectrometry and carbon isotope analysis. By identifying the source of oil and gas, the migration and transportation path of oil and gas were analyzed according to the typical oil and gas reservoirs, and the geochemical migration parameters were optimized to trace the migration and filling path of oil and gas. The following results are presented:the Mesozoic- Cenozoic crude oil in the southern slope of Kuqa presents the characteristics of continental crude oil, such as low density, low viscosity, low solidification point, low sulfur content and high wax content. Crude oil was primarily derived from algae and aquatic planktons, reflecting the sedimentary environment of weak reduction- weak oxidation of maternal materials and the characteristics of mixed kerogen source. The Cretaceous crude oil is mainly derived from lake- facies aquatic organisms, mainly from Triassic lake- facies source rocks. Paleogene crude oil is contributed by Triassic lake- facies source rocks in addition to Jurassic lake- facies source rocks;these are accompanied by Jurassic coal measures hydrocarbon source rocks, which are dominated by terrestrial higher plant inputs. Natural gas is characterized by medium methane content, high heavy hydrocarbon content, high nitrogen content and no hydrogen sulfide. Paleogene natural gas mainly belongs to coal- generated gas, which mainly comes from coal- measured source rocks of the middle and lower Jurassic, and some of the oil- associated types of crude oil mixed with early Triassic lacustrine source rocks.The Mesozoic- Cenozoic complex oil and gas transport systems consisting of sand bodies, unconformities and faults are developed in the region. Today, oil and gas in different formations are the result of migration and transportation of oil and gas from different sources and in different transport systems. The crude oil generated by Triassic source rocks mainly migrates along the unconformity at the bottom of Cretaceous or underlying connected sand bodies that guide to the traps at the lower part of Cretaceous. The natural gas of Jurassic source rocks mainly migrates along the unconformity at the bottom of Paleogene and the underlying super- thick sand bodies to the traps at the bottom of Paleogene. Considering hopane parameter Tm/(Ts+Tm), rearranged hopane parameter C30DH/C30H,methyl dibenzothiophene (MDBT) parameter 4- /1- methyl dibenzothiophene of crude oil and C1/C2 value, iC4/nC4 value and carbon isotope composition of natural gas alkanes, it is proposed that there are two main migration paths from Quele to Yudong tectonic belt from north to south, Yingmaili and Hongqi tectonic belt from northeast to southwest, and one secondary migration path from Quele to Yangtak tectonic belt from west to east. In the next step of oil and gas exploration, the exploration targets on the main migration channels should be selected and deployed according to different oil and gas migration paths.