Marine–terrestrial transitional Permian shales occur throughout South China and have suitable geological and geochemical conditions for shale gas accumulation. However, the Permian shales have not made commercial exploitation, which causes uncertainly for future exploration. In this study, high-pressure methane (CH4) adsorption experiments were carried out on the Permian shales in the Lower Yangtze area, and the influences of total organic carbon (TOC) content and temperature on adsorption parameters were investigated. The characteristics and main controlling factors of methane storage capacity (MSC) of the Permian shales are discussed. The results show that the maximum adsorption and the adsorbed phase density of these Permian samples are positively correlated with TOC contents but negatively correlated with temperatures. The pores of organic matter in shale, especially a large number of micropores and mesopores, can provide important sites for methane storage. Due to underdeveloped pore structure and poor connectivity, the methane adsorption capacities of the Permian shales are significantly lower than those of marine shales. Compared with the Longmaxi shales, the lower porosity and lower methane adsorption of the Permian shales are reasonable explanations for their lower gas-in-place (GIP) contents. It is not suitable to apply the index system of marine shales to the evaluation of marine–terrestrial transitional shales. The further exploration of Permian shales in the study area should be extended to overpressure stable reservoirs with high TOC contents (e.g., >5%), high porosity (e.g., >3%), and deep burial (e.g., >2000 m).