Since the first report in early 1990s, mesoporous silica nanoparticles (MSNs) have progressively attracted the attention of scientists due to their potential applications in physic, energy storage, imaging, and especially in biomedical engineering. Owning the unique physiochemical properties, such as highly porosity, large surface area and pore volume, functionalizable, tunable pore and particle sizes and biocompatibility, and high loading cavity, MSNs offer efficient encapsulation and then controlled release, and in some cases, intracellular delivery of bioactive molecules for biomedical applications. During the last decade, functionalized MSNs that show respond upon the surrounding stimulus changes, such as temperature, pH, redox, light, ultrasound, magnetic or electric fields, enzyme, redox, ROS, glucose, and ATP, or their combinations, have continuously revolutionized their potential applications in biomedical engineering. Therefore, this review focuses on discussion the recent fabrication of functionalized MSNs and their potential applications in drug delivery, therapeutic treatments, diagnostic imaging, and biocatalyst. In addition, some potential clinical applications and challenges will also be discussed.