Heterostructural engineering and three-dimensional architecture construction are effective strategies to optimize the photocatalytic performance of semiconductors. Herein, we integrate these two strategies and controllably synthesize ZnO-BiOI heterostructures with well-defined architectures. Microstructural and surface analysis reveals that the strong electronic interaction between ZnO and Bi3+ ensures a bounded nucleation and growth of BiOI on the surface of ZnO, which leads to the formation of ZnO-BiOI nanorod heterostructures (ZnO-BiOI-NR) with very high dispersion of BiOI on ZnO nanorods. In contrast, when the nucleation and growth of BiOI occurs before reacting with ZnO nanorods, ZnO-BiOI heterostructures (ZnO-BiOI-NF) are composed of BiOI nanoflowers (NFs) and ZnO nanorods. The precise control over the interfaces of ZnO-BiOI heterostructures provides ideal models to investigate the influence of the interfaces on the catalytic performance of heterostructures. It is important to highlight that the photocatalytic activity of ZnO-BiOI-NR is 12 times higher than that of ZnO-BiOI-NF. Mechanism studies suggest that the abundant ZnO-BiOI interfaces in ZnO-BiOI-NR benefit the generation and separation of hole-electron pairs, which consequently improve the catalytic performance.