Transition metal dichalcogenide−fullerene (TMD/fullerene) van der Waals (vdW) heterojunctions are promising for photovoltaic applications due to the intriguing optoelectronic properties of their individual components. However, the fundamental understanding of the photophysical process, especially excited-state charge transfer and recombination, remains insufficient. Here, using ab initio nonadiabatic molecular dynamics, we investigated the photoexcitation dynamics across the interface composed of the MoSe₂ monolayer and C₆₀ molecules and compared it with the WSe₂/C₆₀ heterojunction which has been experimentally demonstrated to be efficient for photovoltaic application. Our simulation results show that MoSe₂/C₆₀ exhibits significantly faster electron transfer and a comparable charge recombination time to WSe₂/C₆₀, demonstrating the more efficient charge separation in the MoSe₂/C₆₀ heterojunction. The difference of electron transfer can be primarily explained in terms of the beneficial energy alignment and the enhanced electron-vibrational interaction. The electron–phonon coupling is stronger for the MoSe₂/C₆₀ heterojunction because the thermal structural fluctuation is stronger due to the presence of lighter Mo and because the donor–acceptor overlap is larger arising from the smaller fluctuation of the interlayer distance. We further showed that the electron transfer in the MoSe₂/C₆₀ heterojunction is several orders of magnitude faster than nonradiative charge recombination. The slow charge recombination is a result of the sufficiently large energy gap and the significantly reduced nonadiabatic couplings. Rapid charge transfer and slow charge recombination ensure that the MoSe₂/C₆₀ heterostructure is an excellent candidate for applications in photovoltaics. Our atomistic investigation provides valuable insights into the photoexcitation dynamics across the interface formed by MoSe₂ and C₆₀, demonstrating the potential of the two components in optimizing the charge separation, which is highly relevant for photovoltaic and optoelectronic applications.