Mesoporous silica nanoparticles (MSNs) combine the benefits of nanomaterials and mesoporous silica materials. This class of materials is characterized by ordered pore structures, controllable pore size, and large surface area. Significant research efforts have been devoted to achieve the control over particle size, morphology, pore size, and mesostructure. In this dissertation, I will describe the synthetic approaches, characterization, and structural control of three types of silica-based nanoparticles (NPs). Firstly, the water-based synthesis of ultrasmall (sub-10 nm) PEGylated gold-silica core-shell NPs is described. These core-shell NPs are composed of an ultrasmall gold core, a thin silica shell, and a polyethylene glycol (PEG) outer layer. The core-shell NPs show long-term stability for nearly a year in both water and PBS buffer solution. The NP suspensions further exhibit good contrast in a microscale computed tomography (micro-CT) scanner. Secondly a type of stimuli-responsive aminated MSNs with shapeshifting behavior is introduced. The shape change can be achieved when MSNs are exposed to water vapor in solid-state form for 24 hours, or when MSN suspensions in ethanol are evaporated at high humidity, or when MSNs are vacuum-dried from water-rich solvents. Under these circumstances, , Finally, the synthesis and detailed characterization of a class of quasicrystalline MSNs is discussed. These MSNs exhibit dodecagonal (12-fold) symmetry with particle sizes below 100 nm.