Infectious or immune diseases have caused serious threat to human health due to their complexity and specificity, and emerging drug delivery systems (DDSs) have evolved into the most promising therapeutic strategy for drug-targeted therapy. Various mesoporous biomaterials are exploited and applied as efficient nanocarriers to loading drugs by virtue of their large surface area, high porosity, and prominent biocompatibility. Nanosized mesoporous nanocarriers show great potential in biomedical research, and it has become the research hotspot in the interdisciplinary field. Herein, recent progress and assembly mechanisms on mesoporous inorganic biomaterials (e.g., silica, carbon, metal oxide) are summarized systematically, and typical functionalization methods (i.e., hybridization, polymerization, and doping) for nanocarriers are also discussed in depth. Particularly, structure-activity relationship and the effect of physicochemical parameters of mesoporous biomaterials, including morphologies (e.g., hollow, core-shell), pore textures (e.g., pore size, pore volume), and surface features (e.g., roughness and hydrophilic/hydrophobic) in DDS application are overviewed and elucidated in detail. As one of the important development directions, advanced stimuli-responsive DDSs (e.g., pH, temperature, redox, ultrasound, light, magnetic field) are highlighted. Finally, the prospect of mesoporous biomaterials in disease therapeutics is stated, and it will open a new spring for the development of mesoporous nanocarriers.