To understand the occurrence of natural gas hydrates in seabed sediments, it is crucial to examine the mechanisms of methane (CH4) hydrate formation in sodium montmorillonite (Na-Mt) systems in the presence of amino acid. Accordingly, this study employed kinetics experiments and molecular dynamics simulations to investigate CH4 hydrate nucleation and growth in an Na-Mt system containing alanine (Ala), leucine (Leu), and phenylalanine (Phe), respectively. Kinetics and Raman experiments showed that, compared with Ala, Leu and Phe enhanced hydrogen bonding between water molecules surrounding Na-Mt. This enhancement was due to the long carbon chain of Leu and the phenyl ring of Phe and facilitated CH4 hydrate formation. Moreover, in the Na-Mt system, Ala reduced CH4 consumption, whereas Leu and Phe increased CH4 consumption. Molecular dynamics simulations revealed that the strength of electrostatic interactions between the negatively charged Na-Mt surface and the functional groups of amino acids affected the distribution of amino acids, thereby altering CH4 aggregation and CH4 hydrate nucleation processes. The strong interaction between Na-Mt and Ala significantly disrupted interfacial interactions between Na-Mt and water molecules. In contrast, the weaker interactions between Na-Mt and Leu and Phe, respectively, meant that these amino acids affected CH4 hydrate nucleation in the bulk-like solution by influencing the arrangement of water molecules. These findings indicate that interfacial interactions between Na-Mt and amino acids play a crucial role in CH4 hydrate formation. Overall, this study generated insights into the formation kinetics and nucleation properties of CH4 hydrates in clay mineral–amino acid complexes that may increase understanding about the occurrence of natural gas hydrates in marine sediments.