The abuse of antibiotics has led to the emergence of antibiotic resistant bacteria and high threats to human health. The search for safe and effective alternatives to traditional antibiotics is growing worldwide. In this article, we report the synthesis of large pore dendritic mesoporous silica nanoparticles (DMSNs) with controllable particle sizes and investigate the relationship between the particle size of DMSNs and their antibacterial enzyme delivery performance. The choice of dual-functional perfluorocarbon anions with both low surface tension and interaction with cationic surfactants enables the synthesis of DMSNs with tunable particle size and pore size. After loading with lysozyme, a naturally occurring antimicrobial enzyme, DMSNs with a large pore size of 22.4 nm and a small particle size of 79 nm show significantly better antibacterial activity compared to either DMSNs with a larger particle size (160 nm) or MSNs with a smaller pore size (2.4 nm) while the other parameter is similar. The optimized DMSNs loaded with lysozyme exhibit total inhibition towards Escherichia coli (E. coli) throughout five days. Our study provides new insights into the controllable synthesis of nano-carriers for antimicrobial protein delivery applications.