ZnO–In₂O₃ (InO) core–shell nanorod heterostructures were synthesized by sputtering InO crystallites on ZnO nanorods. InO shell layers consisting of tapered and prism-shaped InO crystallites were obtained by varying the sputtering deposition duration. The crystalline InO layer on the ZnO nanorods was composed of small tapered InO crystallites and showed a (222) orientation. However, large prism-shaped InO crystallites on ZnO showed multiple crystallographic orientations. The InO shell layer consisting of prism-shaped crystallites had a larger number of crystal defects than the InO shell layer with a tapered morphology. Comparatively, the ZnO–InO heterostructures with a prism-shaped InO shell layer showed oxidizing gas sensing and photoelectrochemical performance superior to those of the heterostructures with a tapered-morphology InO shell layer. The difference in crystal features between the tapered and the prism-shaped InO crystallites explained the observations in this study.