The combination of high-resolution computed tomography (CT) and the real-time sensitive second near-infrared window (NIR-II) fluorescence bioimaging can provide complementary information for the diagnosis, progression and prognosis of gastrointestinal disorders. Ag2Te quantum dots (QDs) are a kind of promising CT/NIR-II fluorescence dual-modal imaging probe due to their high atomic number and narrow bandgap. However, conventional Ag2Te QDs synthesized by oil phase approaches often suffer from complicated steps, harsh reaction conditions, and toxic organic solvents. Herein, we report the synthesis of bovine serum albumin (BSA)-Ag2Te QDs using a biomineralization approach for CT/NIR-II fluorescence dual-modal imaging of the gastrointestinal tract. The BSA-Ag2Te QDs are fabricated in a facile one-pot approach under mild conditions and exhibit homogeneous size, favorable monodispersity, admirable aqueous solubility, excellent X-ray attenuation properties, and outstanding NIR-II fluorescence performance. In vivo imaging experiments show that BSA-Ag2Te QDs can be used in gastrointestinal tract CT/NIR-II dual-modal imaging with high spatiotemporal resolution and sensitivity. In addition, in an intestinal obstruction mouse model, accurate lesion positioning and imaging-guided obstruction relief surgery are successfully realized based on BSA-Ag2Te QDs. Besides, BSA-Ag2Te QDs have outstanding biocompatibility in vitro and in vivo. This study presents a high-performance and biosafe CT/NIR-II fluorescence dual-modal imaging probe for visualizing the gastrointestinal tract in vivo.