In order to elucidate the interaction mechanism between wax and hydrates in oil and gas extraction, molecule dynamics simulations was used to investigate the effects of wax crystals on hydrate nucleation, growth, aggregation, and crystal structure. The results show that wax crystals exhibit a dual role in both promoting and inhibiting hydrate formation. In low-to-medium concentration wax-containing systems, wax crystals attract surrounding methane molecules to their vicinity, thereby increasing methane concentration in the adjacent aqueous phase, which strengthens the driving force of hydrate formation. However, in high-concentration wax systems, the strong adsorption properties of wax molecules lead to the formation of a gas film of methane molecules on their surfaces. In this scenario, the reduced methane concentration in the aqueous phase suppresses hydrate formation. The findings of this study will lay a theoretical foundation for preventing wax-hydrate blockages in oil and gas pipelines.