The Mabei area in the Mahu sag of the Junggar Basin has yielded significant hydrocarbon discoveries in multiple strata, including the Carboniferous, Permian, and Triassic. However, physical properties of crude oil vary spatially and stratigraphically, and the genetic mechanism underlying this differentiation represents a critical geological factor constraining hydrocarbon exploration. In this study, analyses on total hydrocarbon chromatography and biomarker were systematically performed. Based on the differential distribution of crude oil physical properties, the genetic mechanism of spatial differentiation was investigated, and an oil accumulation model for the Mabei area was established. The results show that the chemical composition of crude oil is the fundamental cause of physical property variations. Differences in depositional environment and thermal maturity of source rocks give rise to variations in chemical composition. In addition, multi-stage charging, mixing, and biodegradation further complicate the physical properties of crude oil. The Triassic crude oil in the sag and slope zones features low density, low viscosity, high wax content, and a high freezing point. It has a high proportion of saturated hydrocarbons and a low content of isomeric branched alkanes, indicative of predominantly high-mature oil. This oil was sourced from the high-maturity source rocks of the Fengcheng formation in the sag, migrated upward along faults, and accumulated in shallow reservoirs. The Permian crude oil in the slope zones and the conventional crude oil in the fault zones is characterized by high density, high viscosity, low wax content, and low freezing point. These oils have low saturated hydrocarbon content but abundant isomeric branched alkanes, and are dominated by mature oil, with a minor proportion of high-mature oil. Specifically, the mature oil originated from the source rocks of the Fengcheng formation in the fault and slope zones, forming reservoirs through vertical near-source migration or in-situ accumulation. The high-mature oil, which occurs only in the fault zones, is interpreted to have been sourced from both the Fengcheng and Jiamuhe formations, with lateral migration as the primary transport mechanism. The shallow heavy oil in the fault zones, buried at depths of less than 1,500 m, has a high freezing point and was mostly subjected to biodegradation.