Silica minerals are a kind of important minerals and widespread on the earth’s surface. They play an irreplaceable role in the whole geochemistry and environment processes. The diversity in the crystal structure of SiO2 polymorphs might lead to the heterogeneity in their surface microstructures and properties. As two common SiO2 polymorph minerals in soil and sediments, α-quartz and α-cristobalite have been studied for the effects of their surface heterogeneity on adsorption behaviors toward crystal violet (CV) by batch adsorption experiments in different specific surface areas (SSAs) and at different pH values and temperatures, as well as by X-ray photoelectron spectroscopy (XPS) investigation. Owing to the larger surface site density, the saturated adsorption amount of α-quartz was larger than that of α-cristobalite. It was also indicated by the larger slope of adsorption lines as a function of SSA. The adsorption capacity of both increased with increasing pH and temperature. In the thermodynamic study, the negative ΔG indicated that the adsorption of CV on the surface was spontaneous and the positive ΔH suggested that the reaction was endothermic. The well-fitted Langmuir adsorption isotherms suggested that the CV adsorption was monolayer adsorption. The adsorption interaction force was mainly involved in electrostatic attraction force between the negatively charged surface reactive sites and positively charged N atoms in the dimethylamino groups of CV. The XPS spectra of N 1s showed that the stoichiometric ratio of Nlow/Nhigh changed from lower than 2:1 to about 2:1 as the adsorption changed from the unsaturated to saturated state. The change reflected that the spatial arrangement of adsorbed CV monomer on the mineral surface could be readjusted by lifting the average tilt angle between the average plane of the CV monomer and the sample surface during the adsorption process. Surface heterogeneity of α-quartz and α-cristobalite controlled the different distributions and postures of adsorbed CV monomers on the surface. The CV monomers adsorbed on α-quartz presented a larger average tilt angle because of its larger surface reactive site density, while α-cristobalite did conversely.