Molybdenum trioxide (MoO₃) has been widely studied in the energy storage field due to its various phase states and unique structural advantages. Among them, lamellar α-phase MoO₃ (α-MoO₃) and tunnel-like h-phase MoO₃ (h-MoO₃) have attracted much attention. In this study, we demonstrate that vanadate ion (VO₃^-) can transform α-MoO₃ (a thermodynamically stable phase) to h-MoO₃ (a metastable phase) by altering the connection of [MoO₆] octahedra configurations. h-MoO₃ with VO₃^- inserted (referred to as h-MoO₃-V) as the cathode material for aqueous zinc ion batteries (AZIBs) exhibits excellent Zn²⁺ storage performances. The improvement in electrochemical properties is attributed to the open tunneling structure of the h-MoO₃-V, which offers more active sites for Zn²⁺ (de)intercalation and diffusion. As expected, the Zn//h-MoO₃-V battery delivers specific capacity of 250 mAh·g⁻¹ at 0.1 A·g⁻¹ and rate capability (73% retention from 0.1 to 1 A·g⁻¹, 80 cycles), well exceeding those of Zn//h-MoO₃ and Zn//α-MoO₃ batteries. This study demonstrates that the tunneling structure of h-MoO₃ can be modulated by VO₃^- to enhance the electrochemical properties for AZIBs. Furthermore, it provides valuable insights for the synthesis, development and future applications of h-MoO₃.