Abstract: A conglomerate is an important type of oil and gas reservoir. Analyzing its heterogeneity and genesis is conducive to identifying main controlling factors and hydrocarbon accumulation mechanisms of conglomerate reservoirs, thereby providing guidance for oil and gas reservoir prediction and exploration deployment. This study focuses on two sets of conglomerate reservoirs from the Upper Permian Upper Wuerhe Formation and the Lower Triassic Baikouquan Formation in the Mahu Sag of the Junggar Basin, which are in unconformity contact. Based on core observations, petrographic identification, scanning electron microscopy (SEM), major element analysis, and detrital zircon U-Pb dating, the lithology and reservoir capacity of the two sets of reservoirs were systematically compared. The significant differences in parent rock composition, cement types, and reservoir space and properties of these two reservoirs were identified. The gravels of the Upper Permian Upper Wuerhe Formation in the Mahu Sag of the Junggar Basin were mainly composed of medium-basic igneous rock debris and tuff debris, the cements were mainly zeolite and calcite, and the dominant reservoir space was laumontite dissolution pores. In contrast, the gravels of the Lower Triassic Baikouquan Formation were mainly felsic in composition, the calcite exhibited heterogeneous cementation, and the dominant reservoir space was feldspar dissolution pores. Differences in sediment provenance were the fundamental cause of variations in framework grains and cements between the two sets of reservoirs, and the subsequent acidic fluid activities and differential water and rock interactions further influenced reservoir space types and assemblages. High-quality reservoirs in both formations predominantly developed in subaqueous distributary channel depositional microfacies within the fan-delta front facies belt. Depositional microfacies controlled the original pore structure, while parent rock composition, sedimentary evolution, diagenesis, and fault activities jointly shaped the development characteristics and physical property distribution of the reservoirs.