In this work, the spectral properties of the photo-induced delayed luminescence (DL) from mesenchymal stem cells (MSCs) and their correlation with cell viability were investigated using the single photon counting combined with band-pass filters. The results show that the DL of MSCs has a broad spectral distribution, which covers from 300 nm to 650 nm at least. The DL spectrum is not evenly distributed, but mainly distributed in the range from 400 nm to 550 nm. In addition, the DL spectral distribution remains stable during the DL decay process. Compared with the DL spectra of MSCs with high viability (>80%), those of MSCs with low viability (<30%) show a significant red-shift, referring to the increase in the proportion of 572—650 nm band and the decrease in the proportions of both 315—436 nm band and 413—500 nm band. Furthermore, the degree of the DL spectral red-shift exhibits a monotonous change as MSCs’ viability decreases, and thus can be used as an important indicator for the cell viability assessment.