Infection by pathogens has always been a major threat to human health, and various drugs have been explored and designed to kill pathogens in the past decades. However, pathogens are evolving faster than the development of new antibiotics, and increasing doses are resulting in increasing side effects and toxicity; this has prompted us to exert effort toward the development of advanced drug carriers for precise delivery of antibiotics. In this study, with the involvement of persistent luminescence nanophosphors (PLNPs) as the emission core, we propose an antibiotic nanocarrier for in vivo delivery of vancomycin to intestinal bacteria via bioimaging guidance. The synthesized PLNPs were coated with mesoporous silica for vancomycin adsorption (NPs@SiO2@Van) and used as an efficient nanocarrier for direct vancomycin delivery and in vivo imaging with low cytotoxicity toward MC38 cell lines. Additionally, we detected the luminescence signals of NPs@SiO2@Van during their use as nanocarriers for vancomycin and accurately obtained the biodistribution of NPs@SiO2@Van in situ and in real time with neglectable auto-fluorescence from the animal body. For the first time, bioimaging-guided in vivo drug delivery to gut bacteria was realized in the present work. The outstanding luminescence features and excellent biocompatibility and structural stability of PLNPs may open new horizons in the development of nanocarriers for nano-diagnosis/therapy and in vivo studies of intestinal microorganisms.