Mesoporous silica nanoparticles (MSNs) are promising functional nanomaterials for a variety of biomedical applications, such as bioimaging, drug/gene delivery, and cancer therapy. This is due to their low density, low toxicity, high biocompatibility, large specific surface areas, and excellent thermal and mechanical stability. The past decade has seen rapid advances in the development of MSNs with multiple compartments. These include hierarchical porous structures and core-shell, yolk-shell, and Janus structured particles for efficient diagnosis and therapeutic applications. We review advances in this area, covering the categories of multicompartment MSNs and their synthesis methods, with an emphasis on hierarchical structures and the incorporation of multiple functions. We classify multicompartment mesoporous silica micro/nanostructures, ranging from core-shell and yolk-shell structures to Janus and raspberry-like nanoparticles, and discuss their synthesis methods. We review applications of these multicompartment MSNs, including bioimaging, targeted drug/gene delivery, chemotherapy, phototherapy, and in vitro diagnostics. We also highlight the latest trends and new opportunities.