Recent advancements in morphology control and surface functionalization of mesoporous silica nanoparticles (MSNs) have enhanced the biocompatibility of these materials with high surface areas and pore volumes. Several recent reports have demonstrated that the MSNs can be efficiently internalized by animal and plant cells. The functionalization of MSNs with organic moieties or other nanostructures brings controlled release and molecular recognition capabilities to these mesoporous materials for drug/gene delivery and sensing applications, respectively. Herein, we review recent research progress on the design of functional MSN materials with various mechanisms of controlled release, along with the ability to achieve zero release in the absence of stimuli, and the introduction of new characteristics to enable the use of nonselective molecules as screens for the construction of highly selective sensor systems.