Methane hydrate is a crystalline compound with methane molecules as guest species trapped in host water cages. In this study, we detected methane hydrate with water cages doped by (Caromatic-H)5 clusters, (Caromatic-H)6 clusters, and (3Caliphatic-H2 + 2H2O) clusters using current spectroscopic techniques and differential scanning calorimetry (DSC). Methane molecules are trapped in the doped cages with type sI forming in nanoscale silica gel pores. The relative quantity ratio of host carbon to guest carbon in the doped hydrate sample reaches approximately 3.58. Methane hydrate doped by CH/CH2 group clusters greatly improves the ability of the hydrate unit cell to store methane and increases the stability of methane hydrate. Fast proton diffusion in the doped methane hydrate was confirmed. The results of this study will provide efficient and energy saving technical support for disruptive changes in hydrate storage and transportation of methane gas technology with a doped and dense solid phase.