The strength of natural clay can be improved with epoxy resins. However, nanoscale curing mechanisms remain poorly understood, which is essential for enhancing stability. In this study, molecular dynamics simulation was employed to calculate the quantity of interface hydrogen bonds, adsorption energy, radius of gyration, and mechanical properties of clay cured by diglycidyl ether of bisphenol-A epoxy resin (DGEBA), diglycidyl ether 4,4’-dihydroxy diphenyl sulfone (DGEDDS), and Aliphatic epoxidation of olefin resin (AEOR). Adsorption behavior and mechanical properties of the clay cured by three epoxy resins were investigated: (1) The chain structure of AEOR led to 18.2% more hydrogen bonds than DGEBA and 59.1% more than DGEDDS. (2) The simulated adsorption energies for DGEBA, DGEDDS, and AEOR with kaolinite were 92.59, 98.25, and 116.87 kcal·mol−1, respectively. (3) The bulk and shear modulus of kaolinite increased by 4.93% and 4.80% when using AEOR. The interface stability and mechanical properties of kaolinite were also improved through strong hydrogen bonds and high adsorption energy. (4) The improvement in Young’s modulus of kaolinite was most significant with AEOR, followed by DGEDDS. AEOR excelled in the Z direction, while DGEDDS excelled in the X and Y directions. This research provided a theoretical foundation to effectively improve the properties of clay using epoxy resins.