In-plane sulfur vacancies (Sv) in molybdenum disulfide (MoS) were newly unveiled for CO hydrogenation to methanol, whereas edge Sv were found to facilitate methane formation. Thus, selective exposure and activation of basal plane is crucial for methanol synthesis. Here, we report a mesoporous silica-encapsulated MoS catalysts with fullerene-like structure and atomic copper (Cu/MoS@SiO). The main approach is based on a physically constrained topologic conversion of molybdenum dioxide (MoO) to MoS within silica. The spherical curvature enables the generation of strain and Sv in inert basal plane. More importantly, fullerene-like structure of few-layer MoS can selectively expose in-plane Sv and reduce the exposure of edge Sv. After promotion by atomic copper, the resultant Cu/MoS@SiO exhibits stable specific methanol yield of 6.11 mol mol h with methanol selectivity of 72.5% at 260 °C, much superior to its counterparts lacking the fullerene-like structure and copper decoration. The reaction mechanism and promoting role of copper are investigated by in-situ DRIFTS and in-situ XAS. Theoretical calculations demonstrate that the compressive strain facilitates Sv formation and CO hydrogenation, while tensile strain accelerates the regeneration of active sites, rationalizing the critical role of strain.