Defects in two-dimensional materials profoundly impact the physicochemical properties of the systems, whose characterization is highly desirable at the atomic scale. Here, using spectroscopic imaging scanning tunneling microscopy, we elucidate the vibrational and magnetic states of MoSe antisite and VMo vacancy with different charge states embedded in ultrathin MoSe2 bilayers supported on graphene substrate. Stringent vibronic states with multimode coupling are resolved on the defects. The spectral intensities are tunable with the electron tunneling rates and well-reproduced by theoretical modeling. Moreover, first-principles calculations suggest that the defects host a local magnetic moment of 2 μB in their neutral state, which is directly confirmed by our spin-flip inelastic electron tunneling spectroscopy. Our study deepens the understanding of defect properties and paves the way of defect-engineering material functionalities and spin-catalytic applications.