Cutaneous melanoma is one of the aggressive cancers. Recent studies have shown that Photobiomodulation (PBM) can inhibit the proliferation of melanoma cells. However, it is not clear that the effect of PBM light mode on the inhibition of melanoma cells. Herein, we investigated the difference of influence between continuous wave (CW) and Pulse PBM on B16F10 melanoma cells. Our results suggested that Pulse mode had a more significant inhibition on the viability of B16F10 melanoma cells than CW mode under the PBM light parameter of wavelength, dose, and average irradiance at 457 nm, 1.14 J/cm2, and 0.19 mW/cm2. Besides, we revealed the differentially expressed genes of B16F10 melanoma cells under the various treatments of PBM light mode (not PBM treatment, CW mode, and Pulse mode) by RNA sequencing. Together, our data suggested that Pulse-PBM can improve the effect of PBM on cells significantly and there may be different molecular mechanisms between Pulse and CW mode including anti-proliferative and cell necrosis. The study shed new light on investigating the molecular mechanisms of various PBM light modes on B16F10 melanoma cells.