The non-invasive imaging of the gastrointestinal (GI) tract is highly desired for clinical research due to the various GI tract bacterial infection-induced diseases. To treat GI tract infections, various antibiotics have been used in the clinic. The growing problem of multidrug-resistant bacteria calls for effective antibiotic alternatives. Here, we construct a dual-functional Bi2S3@mSiO2@Ag nanocomposite for simultaneous enhanced X-ray computed tomography (CT) imaging and efficient antibacterial activity in the GI tract. The nanocomposite also has good stability, low cytotoxicity, and negligible hemolysis. Moreover, the investigation of the long-term toxicity and biodistribution of the Bi2S3@mSiO2@Ag nanocomposite after oral administration confirms its safety at the tested dosage. In particular, Ag nanoparticles (NPs) well dispersed on a silica substrate can reduce the antibacterial dosage and enhance the antibacterial activity of the Bi2S3@mSiO2@Ag nanocomposite. Furthermore, we have established bacterially infected enteritis animal models to confirm the antibacterial ability of the nanocomposite. This work opens up a new avenue for the design of a nanotheranostic agent that acts as both a contrast agent for the enhanced visualization of the GI tract and an antibacterial agent as an alternative to antibiotics.