INTRODUCTION: Mesoporous silica nanoparticles (MSNs) feature a high surface area and large pore volume, uniform and tunable pore size, and stable framework; thus, they have been used extensively as drug carriers. AREAS COVERED: The synthesis, classification, and the latest generation of MSNs, drug loading methods, modification of MSNs, pharmacokinetic studies, biocompatibility, and toxicity of MSNs, and their application in drug delivery systems (DDS) are covered in this review. EXPERT OPINION: It is crucial to uncover the mechanism for the formation of MSNs. Before drug loading, the characteristics of MSNs should be taken into consideration. In addition, the porosity, particle size and morphology, surface oxidation and surface functionalization can also influence the in vivo fate of MSNs, which is worthy of further study. Coating MSNs with novel materials may improve their biocompatibility, control the release of drugs loaded into the MSNs or enhance the uptake of the coated MSNs by tumor cells. MSNs can also be used as carriers for combination therapy in the treatment of cancer. Despite the rapid development of MSNs, the biological effects of these biomaterials remain relatively less understood.