Two upper Middle Permian palaeosols, consisting of coal and pyrite intercalated with a 20 cm thick limestone, were found near Mount Emei in the SW Sichuan Basin, China. The macro- and micromorphology and physico-chemical properties, in conjunction with the mineralogical composition of the palaeosol horizons were investigated. This type of palaeosol is common within the Permian intertidal facies of the Upper Yangtze Craton. The section reflects fluctuations within the range of 0–25 m in relative sea-level, with the depositional environment changing from shallow-marine to littoral, followed by tidal-flat to littoral, and finally to continental volcanic rocks, based on a combination of palaeopedological and carbonate microfacies analyses. Such short-term relative sea-level fluctuations in late Middle Permian times in the SW Sichuan Basin of South China are consistent with the long-term falling trend on a global scale in late Middle Permian times, and may be related to regionally variable subsidence and global cooling. The combination of coastal palaeosol and carbonate microfacies analyses is proposed as an additional tool for estimating the amplitude of sea-level changes.