Mesoporous silica nanoparticles (MSNs) have garnered significant attention across various disciplines, including chemistry, physics, and materials science, owing to their distinctive properties and functionalities. Numerous studies have demonstrated that MSNs possess several advantageous characteristics, such as tunable pore sizes, excellent biocompatibility, and a high specific surface area. These attributes render mesoporous silica nanoparticles promising for diverse applications in medical fields, including in vivo targeting, drug delivery, and disease diagnosis. Nevertheless, recent research has indicated that mesoporous silica may induce cellular and tissue toxicity in humans, necessitating further evaluation of its long-term safety. Additionally, parameters such as the shape, particle size, and surface modification of MSNs require careful control to enhance their biodegradability, regulate the circulation time of nanomaterials within the body, and mitigate the immunogenicity of mesoporous silica, thereby facilitating the clinical translation of mesoporous silica nanoparticles. This article reviews the advancements in research concerning the use of mesoporous silica nanomaterials in targeted therapy, drug delivery, and tissue engineering. This work evaluates the potential applications of mesoporous silica materials in the biomedical sector and delineates future research directions for MSNs by examining and summarizing their biological toxicity and associated risks.