The charge excitation and decay pathways of two-dimensional heteroatomic quantum dots (QDs) are affected by the quantum confinement effect, bandgap structure and strong exciton binding energy. Recently, semiconducting transition metal dichalcogenides (TMDs) have been intensively studied; however, the charge dynamics of metallic phase QDs (mQDs) of TMDs remain relatively unknown. Herein, we investigate the photophysical properties of TMD-mQDs of two sizes, where the TMD-mQDs show different charge excitation and decay pathways that are mainly ascribed to the defect states and valence band splitting, resulting in a large Stokes shift and two excitation bands for maximum photoluminescence (PL). Interestingly, the dominant excitation band redshifts as the size increases, and the time-resolved PL peak redshifts at an excitation wavelength of 266 nm in the smaller QDs. Additionally, the lifetime is shortened in the larger QDs. From the structural and theoretical analysis, we discuss that the charge decay pathway in the smaller QDs is predominantly affected by edge oxidation, whereas the vacancies play an important role in the larger QDs.