The terrestrial lacustrine fan delta conglomerate reservoirs in the Triassic Baikouquan Formation (BF) are the primary hydrocarbon exploration targets in the Mahu sag, Junggar Basin, Western China. However, the varying lithofacies and complex diagenesis controlling the reservoir quality remain poorly understood. For the sake of revealing how reservoir quality is associated with sedimentary processes and diagenetic alterations, we used integrated approaches like petrographical analysis, cores description, wireline, X-ray diffraction (XRD), scanning electron microscopy (SEM), mercury intrusion capillary pressure (MICP) and measured petrophysical properties. The results showed that sedimentary processes have considerable control over facies distribution, grain size, and clay content, causing spatial variation of reservoir quality within the fan delta deposits. The coarser grain and high clay content fraction at the base of gravity flow will first settle in the fan delta plain near provenance, whereas the finer grains at the top of flows progressively deposit in the fan delta front areas. From proximal to distal fan delta, a progressive conversion from cohesive muddy debris flow into traction current can be inferred from the variations of lithofacies associations. A total of 8 types of microfacies were identified where the conglomerates of the BF were deposited. The grayish-green fine-grained conglomerates concentrated in the subaqueous distributary channels provide the best reservoir performance, whereas debris flow deposits dominated primarily by muddy debrites occupy the worst reservoir quality because of their highest clay content and coarsest grain size.The dominant diagenetic events include mechanical compaction that continued throughout the entire burial, two phases of quartz cementation, dissolution of unstable components, early and late carbonate cementation, precipitation of authigenic clay minerals, and two phases of hydrocarbon charging. It is unveiled that compaction is the predominant mechanism negatively affecting reservoir quality in the fan delta complex, while the effect of cementation on pore reduction of the conglomerate reservoir is weaker than compaction. Simultaneously, a complex relationship exists between reservoir petrophysical properties within different clay minerals. Dissolution does not significantly improve the permeability of the reservoir because of the partial dissolution which primarily generated intragranular pores with strong heterogeneity and poor connectivity. The most favorable reservoirs occur primarily in the subaqueous distributary channels in the fan delta front, which comprise well-sorted fine-grained conglomerates with well-developed residual intergranular pores and secondary dissolution pores and have undergone two phases of oil charge. This work may provide a useful reference for hydrocarbon exploration of the fan delta systems and regions which have encountered similar sedimentary and diagenetic processes.