Acid activation plays an important role in modifying the microstructure and improving the surface properties of clay minerals. Herein, the microstructural evolution characteristics and surface charge properties of different derived kaolinites were investigated and the relevant mechanism was discussed. Acid activation could gradually expand the interlayer distance of both kaolinite and coal-bearing kaolinite due to the leaching of cations and the following weakened interlayer forces. The structure of kaolinite has a better resistance to acidic attack. Most of the frame structures and functional groups are retained when the acid concentration is 2 mol/L and the treatment time is up to 72 h at room temperature. Acid activation has little effect on dehydroxylation temperature but a greater effect on transformation temperature of ~3–7 °C. The relatively rapid changes of zeta potential indicate stronger protonation and deprotonation reactions in coal-bearing kaolinite. The process could release more acidic sites while maintaining the layered structure, proved the gradual evolution process of macroscopic properties, and complemented that in harsh chemical conditions such as high temperature and acid concentration.