We explore a phase engineering strategy to improve the electrochemical performance of transition metal sulfides (TMSs) in anode materials for lithium-ion batteries (LIBs). A one-pot hydrothermal approach has been employed to synthesize MoS2 nanostructures. MoS2 and MoO3 phases can be readily controlled by straightforward calcination in the (200–300) °C temperature range. An optimized temperature of 250 °C yields a phase-engineered MoO3@MoS2 hybrid, while 200 and 300 °C produce single MoS2 and MoO3 phases. When tested in LIBs anode, the optimized MoO3@MoS2 hybrid outperforms the pristine MoS2 and MoO3 counterparts. With above 99% Coulombic efficiency (CE), the hybrid anode retains its capacity of 564 mAh g−1 after 100 cycles, and maintains a capacity of 278 mAh g−1 at 700 mA g−1 current density. These favorable characteristics are attributed to the formation of MoO3 passivation surface layer on MoS2 and reactive interfaces between the two phases, which facilitate the Li-ion insertion/extraction, successively improving MoO3@MoS2 anode performance.