The evolution of shale reservoirs is mainly related to two functions: mechanical compaction controlled by ground stress and chemical compaction controlled by thermal effect. Thermal simulation experiments were conducted to simulate the chemical compaction of marine-continental transitional shale, and X-ray diffraction (XRD), CO2 adsorption, N2 adsorption and high-pressure mercury injection (MIP) were then used to characterize shale diagenesis and porosity. Moreover, simulations of mechanical compaction adhering to mathematical models were performed, and a shale compaction model was proposed considering clay content and kaolinite proportions. The advantage of this model is that the change in shale compressibility, which is caused by the transformation of clay minerals during thermal evolution, may be considered. The combination of the thermal simulation and compaction model may depict the interactions between chemical and mechanical compaction. Such interactions may then express the pore evolution of shale in actual conditions of formation. Accordingly, the obtained results demonstrated that shales having low kaolinite possess higher porosity at the same burial depth and clay mineral content, proving that other clay minerals such as illite–smectite mixed layers (I/S) and illite are conducive to the development of pores. Shales possessing a high clay mineral content have a higher porosity in shallow layers (< 3500 m) and a lower porosity in deep layers (> 3500 m). Both the amount and location of the increase in porosity differ at different geothermal gradients. High geothermal gradients favor the preservation of high porosity in shale at an appropriate Ro. The pore evolution of the marine-continental transitional shale is divided into five stages. Stage 2 possesses an Ro of 1.0%–1.6% and has high porosity along with a high specific surface area. Stage 3 has an Ro of 1.6%–2.0% and contains a higher porosity with a low specific surface area. Finally, Stage 4 has an Ro of 2.0%–2.9% with a low porosity and high specific surface area.