Cellular uptake of nanoparticles for stem cell labeling/tracking is considered as the most promising method. Recently mesoporous silica nanoparticles (MSNs) are emerging as an idea agent for efficient stem cell labeling. The objective of this study was to evaluate the effect of surface charge on the highly efficient cellular uptake and in vitro cytotoxicity of MSNs in human mesenchymal stem cells (hMSCs). The surface charge was varied by the degree of surface modification with N-trimethoxysilylpropyl-N,N,N-trimethylammonium chloride and the uptake of MSNs was detected by flow cytometry. 3T3-L1 cells were also used to compare the uptake behavior of MSNs between cell types. A clear correlation of positive surface charge and the number of fluorescence-labeled cells was mainly observed in 3T3-L1 cells. In both cells, uptake of unmodified MSNs was inhibited by phenylarsine oxide (PAO) and cytochalasin D (Cyt D) suggesting a clathrin- and an actin-dependent endocytosis were involved. With strongly positive-charged MSNs, the inhibitory effects were observed in 3T3-L1 cells but not in hMSCs. Without regard to the surface charge, uptake of MSNs into both cells did not affect their viability, proliferation, and differentiation. Our results show that MSNs uptake by hMSCs can be regulated by a threshold of positive surface charge but also imply that the modulation of surface charge on MSNs uptake is specific to cell type.