Organic acids are commonly found in soils and sediments, playing an important role in the alteration and weathering of minerals and influencing a series of geochemical processes such as soil fertility, metal cycling and pollutant migration. In order to better comprehend the reaction mechanisms of different layered silicate minerals with organic acids, three minerals with various structure types, namely montmorillonite, kaolinite and muscovite, were investigated in this work. In particular, the effects of interfacial reactions with oxalic acid on the crystal structure, chemical composition, morphology and specific surface area of minerals were compared. The composition and structure of montmorillonite, kaolinite and muscovite during the interfacial reaction with oxalic acid were characterised using powder X-ray diffraction (XRD), scanning electron microscopy (SEM) and inductively coupled plasma-optical emission spectroscopy (ICP-OES) methods. It was shown that Si4+ and Al3+ were dissolved gradually during the interfacial reactions and that the changes in the properties of minerals depended on structural characteristics. After 300 days of the interfacial reactions with oxalic acid, the dissolution percentages of Si4+ and Al3+ in montmorillonite, kaolinite and muscovite were 12.7%, 8.4%, 3.8% and 62.1%, 30.7%, 6.1%, respectively. Moreover, the lamellar morphology of montmorillonite was destroyed upon the interfacial reaction with oxalic acid, and irregular particles with sizes of ~100–500 nm were formed on the surface. The diameter of kaolinite flake particles decreased from 400–1500 nm to 50–400 nm, and the surface of rod-shaped particles was ruptured. The small particles disappeared from the muscovite surface, and the initially sharp edges became blunted. The specific surface area and the total pore volume of montmorillonite and kaolinite increased after the interfacial reaction with oxalic acid, whereas the opposite results were obtained for muscovite. The differential dissolution of the minerals during their interfacial reaction with oxalic acid was mainly related to the differences between cation occupancies, structural types, chemical bond strengths and specific surface areas.