Natural gas hydrate in marine sediments is a promising energy resource, while the atomistic level understanding of its formation on the organomineral complex remains limited. Microsecond molecular dynamics simulations were performed to investigate the methane hydrate growth in the sodium montmorillonite interlayer in the presence of natural sediment organic matter [leonardite humic acid (LHA)] at mass concentrations of 2 and 11%. The hydrate growth was characterized by the global and local four-body order parameter, surface distribution function, snapshots of molecular configurations, and face-saturated incomplete cage analysis. It clearly demonstrated the kinetic inhibition effects of LHA on hydrate formation on clay minerals, especially when the self-aggregation of LHA took place at a high concentration. Overall results highlighted the role of methane adsorption on LHA aggregates on the observed inhibition phenomenon, which changed the pathway of gas molecules by complex dynamic processes, such as aggregate deformation, cage break, and cage reformation.