Developing high-temperature metallic glass thin films (MGTFs) with excellent combination properties is crucial for extending the practical applications of metallic glasses. A high-temperature multicomponent Mo-based MGTF with tunable microstructure prepared by single-target magnetron sputtering was presented in this study. Corresponding mechanical behaviors and thermal stability of MGTFs related to microstructure are systemically explored. By adjusting deposition parameters (pressure and power), the microstructure of as-deposited MGTFs can be altered from the dense homogeneous type to the loose nanoglass type. Such structure evolution can be explained by the competition between the surface diffusion and geometric shadowing effect. MGTFs with dense microstructure possess smaller surface roughness, higher hardness, higher Young’s modulus, and better wear resistance. Moreover, they also possess higher thermal stability where the fully amorphous structure and smooth surface can be well maintained after vacuum annealing at 1123 K for 30 min. By contrast, the MGTF with nanoglass microstructure shows inferior mechanical properties and thermal stability due to plentiful loose interface regions, providing abundant free volumes during deformation and acting as favorable crystal nucleation sites during annealing. The correlation between the microstructure and properties of as-deposited MGTFs is clarified with the universal scaling law of glasses. The annealing treatment distinctly increases the hardness and Young’s modulus of MGTFs. Meanwhile, after annealing, pop-in behaviors occur in the as-annealed MGTFs with dense microstructure but not in the as-annealed MGTF with nanoglass microstructure during the nanoindentation. These phenomena can be rationalized by the annihilation of free volumes during annealing and the evolution of the dynamical variable, shear transition zone, for the plastic deformation in MGTFs.