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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.