Abstract: Natural gas hydrates widely accumulate in submarine sediments composed of clay minerals. However, due to the complex physiochemistry and micron-sized particles of clay minerals, their effects on methane hydrate (MH) formation and dissociation are still in controversy. In this study, montmorillonite and illite were separately mixed with quartz sand to investigate their effects on MH formation and dissociation. The microstructure of synthesized samples was observed by cryo-SEM innovatively to understand the effects of montmorillonite and illite on MH phase transition in micron scale. Results show that montmorillonite and illite both show the inhibition on MH formation kinetics and water-to-hydrate conversion, and illite shows a stronger inhibition. The 10 wt% montmorillonite addition significantly retards MH formation rate, and the 20 wt% montmorillonite has a less inhibition on the rate. The increase of illite mass ratio (0–20 wt%) retards the rate of MH formation. As the content of clay minerals increase, the water-to-hydrate conversion decreases. Cryo-SEM images presented that montmorillonite aggregates separate as individual clusters while illite particles pack as face-to-face configuration under the interaction with water. The surface-overlapped illite aggregates would make sediments pack tightly, hinder the contact between gas and water, and result in the more significant inhibition on MH formation kinetics. Under the depressurization method, the addition of clay minerals facilitates MH dissociation rate. Physicochemical properties of clay minerals and MH distribution in the pore space lead to the faster dissociation rate in clay-containing sediments. The results of this study would provide beneficial guides on geological investigations and optimizing strategies of natural gas production in marine hydrate-bearing sediments.