Vanadium-based compounds are highly regarded as potential cathodes for aqueous zinc-ion batteries (AZIBs) owing to the high theoretical capacity, diverse structural frameworks and abundant oxidation states. Nevertheless, the challenges such as slow diffusion kinetics, low electrical conductivity and inadequate structural stability restrict their further development. Herein, yolk shell-like SiO2-coated V2O3/VN heterojunction microspheres (VON@SiO2) are synthesized through a hydrothermal method followed by annealing and subsequent SiO2 coating. As an advanced cathode for AZIBs, the construction of V2O3/VN heterojunction effectively exposes reactive sites, leads to the reduction in interfacial charge transfer resistance, and thus improves the ion diffusion kinetics, while the surface coating of SiO2 is beneficial for enhancing the structural stability of the material and further reduces the capacity fading. Additionally, the micromorphology of porous yolk shell-like microspheres self-assembled by nanoparticles contributes to the complete penetration of electrolyte and greatly exposing reactive sites. Based on synergistic engineering of heterojunction, surface coating and porous shell-like micromorphology, the synthesized VON@SiO2 delivers excellent specific capacities of 483.5 mAh g−1 at 0.5 A g−1 and 294 mAh g−1 at 10 A g−1, and exhibits impressive cycling performance with 94 % of capacity retention after 1000 cycles at 10 A g−1. Further, in-situ XRD and ex-situ XPS reveals the mechanism of zinc ion storage. This work offers a valuable reference into the development of high-performance cathode materials for AZIBs by co-engineering of heterojunction, surface coating and micromorphology optimization.