Herein, three kinds of mesoporous silica nanoparticles (BMSs) were biomimetically synthesized by using heterocyclic amino acid derivatives as template and their the basic capacity in being drug carriers that covered structure, wettability, degradation, brain uptake, hemocompatibility and toxicity were systematically evaluated. The results indicated that BMSs were kinds of spherical nanoparticles with good biocompatibility. Their in vitro and in vivo behaviors, including degradation, biodistribution and biocompatibility were mainly governed by the wettability which was closely related to the structure and pore diameter of mesoporous silica nanoparticles. BMSs can degrade completely under simulated physiological environments through a time period of 2–13 weeks. They showed the tendency of brain distribution, and the distribution amount peaked at 4 h post administration. Particularly, Trp-BMS (BMS templated by C 16 -L-tryptophan) with the largest amount of –OH groups on the surface exhibited highest wettability, fastest degradation rate and the lowest brain distribution ability. Besides, His-BMS (BMS templated by C 16 -L-histidine) and Pro-BMS (BMS templated by C 16 -L-poline) were silica materials with good biocompatibility. Both in vitro and in vivo studies uncovered no significantly toxicity for BMSs and they were proved to be safe when they circulated into the blood. However, Trp-BMS might induce severe hemolysis and cell cycle arrest due to the high wettability. It is believed that appropriate wettability is required for the in vivo application of nanomaterials and the in vivo evaluation of mesoporous silica nanoparticles will provide useful information for understanding the underlining toxicity of biomaterials and bring new insights on designing efficient drug delivery systems.