The successful application of mesoporous silica nanomaterials (MSNs) in biomedical fields requires careful consideration of their spatial dimensions, biofunctionality, specific cellular uptake efficiency, biocompatibility and targeting delivery efficacy. A deep understanding of the interactions between MSNs and biological systems is thus of significant importance. To this end, over the past few decades, studies aimed at synthesis of MSNs with controlled size, shape and surface chemistry properties and exploring the roles of these properties on in vitro and in vivo biological performance have been conducted. These studies provide new and foundational information for engineering the next generation of mesoporous silica-based nanoscale devices. This review highlights the current progress on the controlled synthesis of size, shape and surface chemistry tuneable MSNs, emphasises the roles of size, shape and surface chemistry on biological systems with a special focus on the direct comparison studies, and discusses the emerging design paradigm for building mesoporous silica-based particulate systems.