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This thesis involves synthesis, derivatization and biomedical applications of mesoporous silica nanoparticles (MSNs) based delivery systems. Chapter 1 introduces the background of MSNs including the advantages of MSNs, modification on MSNs for multifunctionality; formation mechanism, a typical synthesis condition for MCM-41 and following characterizaitons. In chapter 2 & 3, the synthesis and application of target moiety functionalized MSNs for gene therapy in vitro and in vivo are introduced. Chapters 4, & 5 introduce the relevant studies of utilizing MSN based delivery system for the treatment of infectious disease, from a pharmacokinetic study of moxifloxacin delivered by MSNs via different routes, to the enhanced efficacy of MSN based treatment by materials optimizations via inhalation administration route. Chapter 6 discusses the study of a general synthesis method for pore enlargement in various types of MSNs. In Chapter 7, the design and preparation of a thin film consist of ultra large pore-sized mesoporous silica spheres and polymer template macropores is illustrated. Overall, these chapters demonstrate the successful engineering of mesoporous silica nanoparticles and materials optimization and their enhanced performance in biological applications from in vivo tumor shrinkage by gene delivery to antibiotics delivery for enhanced bacterial killing efficacy in mouse model.