Methane hydrate is a promising energy resource widely occurring in the world, but the formation and distribution of methane hydrate in marine sediments with complex minerals remains unclear. Due to the small pore space and fine-grained size of clay minerals, the contact relationship between methane hydrate and clay mineral surface under excess water has not been characterized fully, which is required to investigate the mineral effect on methane hydrate formation. In this study, cryo-SEM was applied to observe the distribution of methane hydrate synthesized in pure quartz sands and the quartz sands mixed with montmorillonite or illite separately. According to the results of the research, methane hydrate dispersedly forms in the pore space away from and on the surface of quartz under a local excess water condition. In addition, methane hydrate occurs away from montmorillonite in pores with excess water and contacts the edge of montmorillonite under a local excess-gas condition. Moreover, methane hydrate was only observed to form away from illite aggregates in the pore with residual water. Montmorillonite and illite influence the preferable distribution of methane hydrate to occur away from mineral surface in excess water condition. In the sediments composed of different minerals, methane hydrate forms stochastically in the pore space and grows up individually. As a result, the findings of this study significantly expand the understanding of the formation and distribution of methane hydrate in marine sediments and the prediction of physical properties of hydrate-bearing sediments, and provide insights into natural gas hydrate exploration and production.