Deep-water areas have become a hotspot for global hydrocarbon exploration. In the deep-water area of the Northern South China Sea, a complete set of source rocks, reservoir rocks, and caprock represents a good oil and gas exploration prospect. The Pearl River Mouth basin, an important exploration target in this area, has a wide range of geothermal gradients. However, the mechanism by which the geothermal gradient influences reservoir quality remains unclear, which severely restricts future exploration. We observed that the reduction rates in the porosity and permeability with increasing burial depth and stratum temperature are more rapid in high geothermal gradient areas. The stratum temperature affects the process of diagenesis and the reservoir quality by changing the grain compressive strength, solubility, and precipitation of minerals and clay minerals transformations. With a comparison the crustal extensional thinning histories of different geothermal gradient areas, this study elucidates the comprehensive factors controlling the decreases rates of reservoir porosity and permeability. These findings explain the different evolutions of reservoirs in areas with different geothermal gradients.