The novel 3D porous core-shell vanadium oxide microspheres (CS–V2O5) were successfully prepared through a simple in-situ hydrothermal growth strategy followed by annealed in the air. The obtained CS-V2O5 with high porosity was assembled by many nanoparticles, which can not only provided more active sites, possessed highly enrichment ability, but also offered abundant ions transport channels, effectively shortened the ions diffusion distance and facilitated the rapid transport of electrolyte ions. Square wave anodic stripping voltammetry (SWASV) study showed the CS-V2O5 modified electrode (CS–V2O5/GCE) displayed enhanced electrochemical activity for detecting thallium (Tl+) and indium (In3+) ions synchronously due to the desirable structural property compared with V2O5 nanoparticles (NPs) and V2O5 nanorods (NRs). As a result, the linear range of Tl+ and In3+ was from 1.0 μg L−1 to 50.0 μg L−1 and the detection limit (LOD, S/N = 3) can arrived at 0.1 μg L−1. Furthermore, the developed sensor exhibited superior stability, satisfactory reproducibility, and provided a new approach for the construction of high-performance electrochemical sensor towards toxic metal ions.