The influence of organic solvents on the structural integrity and properties of activated kaolinite were compared and analyzed via characterization techniques and molecular dynamics (MD) simulation. The results revealed that the organic intercalators can be easily inserted into the interlayer spaces of activated kaolinite within a short time of the wet ball milling. The DMSO intercalated kaolinites maintained structural integrity due to the high intercalation rate and the excellent buffering effect against the crushing force of milling during the delamination/exfoliation process. The delaminated layers of the DMSO–kaolinite complex exhibited a high specific surface area of 99.12 m2/g and a low average thickness of 35.21 nm. The calculated elastic properties of the organo-kaolinite complex manifested the intercalation of DMSO into a kaolinite interlayer, which could improve the compressibility and structural integrity of kaolinite nanosheets. The DMSO–kaolinite complex was easier to peel off when compared to the other organic intercalators due to its more intercalated molecules.