Efficient occlusion of particulate additives into a single crystal has garnered an ever-increasing attention in materials science because it offers a counter-intuitive yet powerful platform to make crystalline nanocomposite materials with emerging properties. However, precisely controlling the spatial distribution of the guest additives within a host crystal remains highly challenging. We herein demonstrate a unique, straightforward method to engineer the spatial distribution of copolymer nanoparticles within calcite (CaCO3) single crystals by judiciously adjusting initial [Ca2+] concentration used for the calcite precipitation. More specifically, polymerization-induced self-assembly is employed to synthesize well-defined and highly anionic poly(3-sulfopropyl methacrylate potassium)41-block-poly(benzyl methacrylate)500 [PSPMA41-PBzMA500] diblock copolymer nanoparticles, which are subsequently used as model additives during the growth of calcite crystals. Impressively, such guest nanoparticles are preferentially occluded into specific regions of calcite depending on the initial [Ca2+] concentration. These unprecedented phenomena are most probably caused by dynamic change in electrostatic interaction between Ca2+ ions and PSPMA41 chains based on systematic investigations. This study not only showcases a significant advancement in controlling the spatial distribution of guest nanoparticles within host crystals, enabling the internal structure of composite crystals to be rationally tailored via a spatioselective occlusion strategy, but also provides new insights into biomineralization.