Based on the nonadiabatic molecular dynamics (NAMD) simulations and the first-principles calculations, we explore the overall water-splitting schemes and the photogenerated carrier dynamics for two configurations (CG and CyG) of the CrS3/GeSe van der Waals heterostructures. The photocatalytic direct Z-schemes and carrier migration pathways for hydrogen and oxygen evolution reactions (HER/OER) are constructed based on the electronic properties. The solar-to-hydrogen efficiency (η'STH values) of the schemes can reach 10.60% and 10.17% and further rise under tensile strain. The NAMD results demonstrate similar transfer times of the electron/hole for HER/OER and more rapid electron-hole recombination in CG enables it to be superior to CyG in photocatalytic performance. Moreover, the Gibbs free energy indicates that both the HERs and OERs turn to spontaneously proceed with CG and CyG at pH = 0-12.37 and pH = 2.55-11.01, respectively. These facts reveal that the CrS3/GeSe heterostructure is promising in photocatalytic overall water splitting.