The biomedical applications of mesoporous silica nanoparticles (MSNs) as efficient drug delivery carriers have attracted great attention in the last decade. The structure, morphology, size, and surface properties of MSNs have been found to be facilely tunable for the purposes of drug loading, controlled drug release and delivery, and multifuctionalization. Meanwhile, the biosafety and in vivo drug efficiency of MSN-based nano drug delivery systems (nano-DDSs), involving biocompatibility (including cytotoxicity, blood and tissue compatibility) and pharmacokinetics (including biodistribution, biodegradation, retention, excretion, blood circulation) are also drawing increasing attention because of their clinical application prospects. Herein, we review the most recent research progresses on the synthesis, controlled drug release and delivery, pharmacokinetics and biocompatibility of MSNs.