Mesoporous silica nanoparticles are reported as adjuvants in nanovaccines in generating robust antigen-specific immunity. However, the effect of surface chemistry in initiating and modulating the immune response remains largely unexplored. In this study, mesoporous silica nanorods (MSNRs) are modified with -NH2 and -C-18 groups to investigate the influence of surface functional groups (-OH, -NH2, and -C-18) on their adjuvant efficacy. It is found that compared to -OH and -NH2 groups, the hydrophobic -C-18 modification significantly enhances antigen uptake by antigen presenting cells and endosomal-lysosomal escape in vitro, dendritic cells, and macrophages maturation ex vivo, and elicits secretion of interferon-gamma level and antibody response in immunized mice. Moreover, bare MSNR and MSNR -NH2 exhibit T-helper 2 biased immune response, while MSNR -C-18 shows a T-helper 1 biased immune response. These findings suggest that the surface chemistry of nanostructured adjuvants has profound impact on the immune response, which provides useful guidance for the design of effective nanomaterial based vaccines.