For the first time, a systematic study using density functional theory (DFT) has been employed to survey the synergistic effect of α-MoO3@MoS2 with the aim of gaining insights into the role of this heterogeneous structure in a relevant photocatalytic reaction. The geometry, electronic structures and the band edge positions of the α-MoO3@MoS2 composite were computed to explore the characteristics of the heterojunction. This revealed that the established heterogeneous structure could facilitate the separation of the photoinduced carriers into two parts around the interface. The photoinduced electron carriers injected into the conduction band minimum (CBM) of α-MoO3 from the CBM of MoS2 while the hole carriers transferred from the valence band maximum (VBM) of α-MoO3 to the VBM of MoS2. This separation process could markedly restrain the photogenerated electron-hole pair recombination and was further verified by photocurrent and photoluminescence (PL) surveys. Based on the results obtained from computation, we then synthesized the α-MoO3@MoS2 hybrid rod@sphere structure via a facile two-step hydrothermal method. A reasonable formation mechanism of this rod@sphere structured composite was proposed. The enhanced photocatalytic performance originated from the synergistic effect between α-MoO3 and MoS2. On the one hand, the unique structural characteristics of the composite possessed massive MoS2 spheres closely attached to α-MoO3 rods. On the other hand, the staggered type-II band formation also contributed to the effective separation of photoinduced carriers and thus the corresponding photocatalytic activity was far superior to that of the pristine α-MoO3/MoS2 structures. In brief, the general analyses could fully explain the inner mechanism for the improved photocatalytic activity of the composite structure and provide a reference for the research of composite structures in the future.