Spinel-type materials are promising for the cathodes in rechargeable aqueous zinc batteries. Herein, Zn₃V₃O₈ is synthesized via a simple solid-state reaction method. By tuning the Zn(CF₃SO₃)₂ concentration in electrolytes and the cell voltage ranges, improved electrochemical performance of Zn₃V₃O₈ can be achieved. The optimized test conditions give rise to progressive structure evolution from bulk to nano-crystalline spinel, which leads to capacity activation in the first few cycles and stable cycling performance afterward. Furthermore, the energy storage mechanism in this nano-crystalline spinel is interpreted as the co-intercalation of zinc ions and protons with some water. This work provides a new viewpoint of the structure evolution and correlated energy storage mechanism in spinel-type host materials, which would benefit the design and development of next-generation batteries.