Unlike the release pressure process in shale gas exploitation, in this study, the concentration diffusion process is deeply discussed under constant temperature-pressure conditions, which aims to evaluate the preservation conditions of shale gas reservoirs in combination with isotopic fractionation characteristics. The isobaric diffusion experiment emphasized that decreasing pressure can lead to enhanced diffusion and isotope fractionation. The established mathematical model not only confirms the results of the simulating experiment, but also suggests that the contributions of Fick, Knudsen and surface diffusion to the migration of methane (including 12CH4 and 13CH4) vary in the geological evolution of shale reservoirs, which are mainly controlled by the pore system and gas pressure. Based on the analysis of specific samples of Longmaxi shale (r = 11.7 nm) and Niutitang shale (r = 1.3 nm), we propose that: 1) high pressure condition (> 20 MPa) can significantly limit Knudsen diffusion, which is the reason for reducing the total diffusion coefficient (DTotal) and isotope fractionation, while low pressure (< 10 MPa) and small pore radius (ca. 1 nm) can strengthen the fractionation; 2) pore connectivity and heterogeneity can lead to an order of magnitude change in DTotal, while the influence of temperature is relatively small. According to the mathematical model, it can be expected that enhanced dissipation intensity and isotope fractionation of shale gas may occur in the process of basin uplift and pressure relief, which can potentially be used for the evaluation of reservoir preservation.