The western Qaidam Basin is rich in oil and gas resources, constituting over 90% of the total oil and gas resources in the whole basin. However, the regional distribution characteristics of molecular markers of crude oil and the petroleum system elements relevant to the distribution of oil and gas in the northwest Qaidam Basin are still unclear, which restricts further exploration of oil and gas reservoirs. A total of 38 crude oils were collected from the Xiaoliangshan Sag and Mangya Sag in the northwest Qaidam Basin and analyzed by gas chromatography-mass spectrometry (GC-MS). The indicators of sedimentary environment, organic matter source, and thermal maturity show regular changes from the west to the east in the Xiaoliangshan Sag and Mangya Sag. The nC21 -/nC22 +, n(C21 + C22)/n(C28 + C29), and C27-C28-C29 regular sterane distribution characteristics indicate that the input proportion of lower aquatic organisms in source rocks (E3-N1) gradually increases, while the input proportion of terrigenous organic matter gradually decreases. The triaromatic dinosterane index (TDSI) and methyltriaromatic steroid index (MTDSI) indicate that the input proportion of dinoflagellates gradually increases. The gradual increase in the Pr/Ph ratio indicates a decrease in the reducibility of the sedimentary environment of source rocks. The gammacerane index (Ga/C30H) and methylated-2-methyltrimethyltride-cylchromans (MTTCs) indicate that the degree of stratification and salinity of water body gradually decrease. A total of 23 thermal maturity parameters indicate that crude oil is in a mature evolution stage, and the thermal maturity of crude oil increases with depth, indicating that there are the characteristics of hydrocarbon accumulation close to source rocks. The variation features of sedimentary environment, organic matter origin, and thermal maturity indicators from the west to the east in the Xiaoliangshan Sag and Mangya Sag are controlled by the sedimentary structure characteristics of the study area.