Fractures are the main reservoir space in basement weathering crusts and control the development of dissolution/alteration pores. A clear understanding of the main factors controlling fracture formation is needed to accurately predict reservoir characteristics. In this study, the reservoir characteristics along with the vertical zonation and thermal history of basement weathering crust were studied through lithology, mineral identification, porosity and permeability tests, nuclear magnetic resonance (T2), whole-rock analysis, and fission-track dating based on core samples, cuttings, and imaging logging data. Under the constraints of the Anderson model, the formation stages and timing of fractures were analyzed according to the regional stress field, fracture strike, fracture filling characteristics, and rock mechanical properties. The results revealed tensile structural fractures, shear structural fractures, weathering micro-fractures, alteration fractures, and intracrystalline alteration pores in the weathering crust of the Pre-Cenozoic basement in Lishui Sag. The reservoirs were characterized by low porosity, low permeability, and small pore diameter. The reservoir quality of granite was better than that of gneiss. The weathering crust could be divided into four zones: the soil layer, weathering dissolution zone, weathering fracture zone, and bedrock zone. The thickness of the soil layer and weathering dissolution zone were small. Four stages of fractures were identified: Yandang movement shear fractures, Paleocene tension structural fractures, Huagang movement shear fractures, and Longjing movement shear fractures. The main stage of basement fracture formation differed between the Lingfeng buried hill zone and Xianqiao structural zone. Considering the influence of the temperature and pressure environment on the rock’s mechanical properties, the differential fracture formation is related to the lithology, the coupling between the uplifted and exposed basement histories, and the tectonic stress field. Combined with the thermal histories of the Lingfeng buried hill zone and Xianqiao structural zone, the results suggest that the Lingfeng buried hill granite is favorable for basement fractures in Lishui Sag. Overall, this paper provides a novel method for analyzing the stages of fracture formation.