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Intercalation and surface modification of clays with surfactants are the essential process to tailor the clays’ surface chemistry for their extended applications. A full understanding of the interaction mechanism of surfactants with clay surfaces is crucial to engineer clay surfaces for meeting a particular requirement of industrial applications. In this study, the thermodynamic mechanism involved in the intercalation and surface modification of methanol preintercalated kaolinite by three representative alkane surfactants with different head groups, dodecylamine, cetyltrimethylammonium chloride (CTAC), and sodium stearate, were investigated using the adaptive biasing force accelerated molecular dynamics simulations. In addition, the interaction energies of surfactants with an interlayer environment (alumina surface, siloxane surface, and interlayer methanol) of methanol preintercalated kaolinite were also calculated. It was found that the intercalation free energy of CTAC with a cationic head group was relatively larger than that of stearate with an anionic head group and dodecylamine with a neutral head group. The attractive electrostatic and van der Waals interactions of surfactants with an interlayer environment contributed to the intercalation and surface modification process with the electrostatic force playing the significant role. This study revealed the underlying mechanism involved in the intercalation and surface modification process of methanol preintercalated kaolinite by surfactants, which can help in further design of kaolinite-based organic clays with desired properties for specific applications.