Recent exploration efforts in the Qiongdongnan Basin have revealed hydrocarbon resources within granitic basement rocks in buried hill traps. However, the formation mechanisms and primary controlling factors of these reservoirs remain poorly understood. In this study, we utilized data from six wells in the Qiongdongnan Basin, including sidewall cores, thin sections, imaging logging, and seismic reflection profiles, to analyze the petrological characteristics, pore systems, and fracture networks of the deep basement reservoir. The aim of our study was to elucidate the reservoir formation mechanisms and identify the key controlling factors. The results indicate that the basement lithology is predominantly granitoid, intruded during the late Permian to Triassic. These rocks are characterized by high felsic mineral content (exceeding 90% on average), with them possessing favorable brittleness and solubility properties. Fractures identified from sidewall cores and interpreted from image logging can be categorized into two main groups: (1) NE-SW trending conjugate shear fractures with sharp dip angles and (2) NW-SE trending conjugate shear fractures with sharp angles. An integrated analysis of regional tectonic stress fields suggests that the NE-trending fractures and associated faults were formed by compressional stresses related to the Indosinian closure of the ancient Tethys Ocean. In contrast, the NW-trending fractures and related faults resulted from southeast-directed compressional stresses during the Yanshanian subduction event. During the subsequent Cenozoic extensional phase, these fractures were reactivated, creating effective storage spaces for hydrocarbons. The presence of calcite and siliceous veins within the reservoir indicates the influence of meteoric water and magmatic–hydrothermal fluid activities. Meteoric water weathering exerted a depth-dependent dissolution effect on feldspathoid minerals, leading to the formation of fracture-related pores near the top of the buried hill trap during the Mesozoic exposure period. Consequently, the combination of high-density fractures and dissolution pores forms a vertically layered reservoir within the buried hill trap. The distribution of potential hydrocarbon targets in the granitic basement is closely linked to the surrounding tectonic framework.