In spite of many studies of laterite origins in various parts of the world, the origin of laterite in the middle to lower reaches of the Yangtze River is still a topic of debate, thus leaving doubts about the prevailing environmental and climatic conditions at the time. The purpose of this study was to provide greater understanding of this subject by examining in more detail the associated mineralogical evolution, i.e. clay mineral composition, structural characteristics of clays in various beds with different degrees of weathering along the laterite profile, and the alteration mechanisms during the pedogenic process in tropical to semitropical climate conditions. High-resolution transmission electron microscopy (HTEM), X-ray diffraction, and wavelength dispersive X-ray fluorescence spectrometry were used to characterize the samples in order to link clay mineralogy in various beds with different degrees of weathering along the laterite profile to the formation and origin of laterites in the region. The laterite profile displayed a distinct layered structure and was divided into a saprolite (B4), a light colored net-like clay bed (B3), a brown-red gravelly clay bed (B2), and a dark-brown topsoil (B1), respectively, from bottom to top. The clay mineral assemblage of beds B1 and B2 was illite, kaolinite, and chlorite, while that of beds B3 and B4 was mainly kaolinite with minor illite. The bimodal particle-size distribution of clay minerals in the laterite profile indicated that fine-grained particles could have been produced by partial dissolution and decomposition of coarse-grained ones. Examination by HRTEM revealed that fine-grained particles usually occurred as X-ray amorphous materials in the upper soil beds, but with euhedral morphology in the lower portions, suggesting that the fine-grained particles in the lower soil beds might be partially neoformed during the weathering process. Amorphous spots occurred frequently in kaolinite crystals in the upper soil beds, while the structure of kaolinite was well preserved, with a well defined lattice-fringe image. The illite crystallinity index exhibited a trend of downward decrease, while the values of the chemical index of alteration (CIA = Al2O3/(Al2O3+ CaO+ K2O+ Na2O) × 100%) of the soil profile showed a trend of downward increase. Samples of the upper soil beds, B1 and B2, had comparable SiO2/Al2O3 ratios of 5.37–6.22, while those of the lower beds, B3 and B4, had significantly smaller SiO2/Al2O3 ratios of 1.92–3.98, suggesting that the latter had a greater degree of weathering than the former, in reasonable agreement with the results of the illite crystallinity and CIA index. In addition, samples from B1 and B2 had similar TiO2/Al2O3 ratios of 0.042–0.053, while those from B3 and B4 had comparable TiO2/Al2O3 ratios of 0.021–0.033, comparable to the value 0.020 of the bedrock, and were notably smaller than the upper soil beds, indicating that materials of the upper soil beds, B1 and B2, had a different origin from the lower soil beds. The upper bed was probably derived from eolian accumulation due to intensification of the winter monsoon and aridity in central Asia and was modified by intense chemical weathering since the late Pleistocene, while the lower bed originated from an in situ weathering of the underlying argillaceous limestone.