Geosynthetic clay liners (GCLs) are often used as anti-seepage systems in landfills and at the bottom of tailing ponds. The anti-seepage performance of GCL will change under different temperatures. In this study, bentonite was mixed with test solutions at different temperatures to measure the basic performance indexes of bentonite components and analyze the permeability. The composition and micro-structure of bentonite at different temperatures were analyzed by X-ray diffraction, X-ray fluorescence spectrum, and SEM, and the change rule of permeability property with the mine leachates at different temperatures was understood by combining the macro-measured parameters with the microscopic analysis results. The research results indicate that the fluid loss of two bentonites increased with the increasing temperature due to the inhibition of ion exchange between bentonite and mixture by the increased temperature. The swelling index of the bentonite increased at high temperatures. The micro-structure analysis showed the increase of the pore size attributed to high temperature, and the uneven distribution of the pore size resulted in the increase of the intrinsic permeability. The study would provide the reference for the application of GCL in mining.