X-ray computed tomography (CT) imaging can be used to reveal the three-dimensional structure of deep tissue with high spatial resolution. However, it cannot reveal molecular or cellular changes, and has great limitations in terms of specificity and sensitivity. Fluorescence imaging technology is one of the main methods used for the study of molecular events in vivo and has important applications in life science research. Therefore, the combination of CT and fluorescence imaging is an ideal dual-modal molecular imaging method, which can provide data on both molecular function and tissue structure, and has important research value. In a previous study, Bi2S3 nanoparticles were wrapped with quantum dots in SiO2 to generate CT and fluorescence imaging. However, this type of probe led to low survival and caused innegligible in vivo toxicity in mice. Therefore, it is necessary to develop new multifunctional probes that demonstrate biocompatibility and safety in vivo. A polyethylene glycol-phospholipid bilayer structure was used to synthesize hybrid clusters containing hydrophobic Bi2S3 nanoparticles and quantum dots for combined CT/fluorescence imaging. Mean particle size, polydispersity index, and zeta potential were used to study the stability over an 8-week test period. In vivo CT and fluorescence imaging experiments were performed, and the in vivo safety of the probe was evaluated, using histopathological, biochemical, and blood analyses. The probe distinctly enhanced the CT contrast and had fluorescence imaging capability. In addition, the nanocomposite hybrid clusters showed a longer circulation time (>4 h) than iobitridol. The results also showed that the Bi2S3-QD@DSPE probe had good biocompatibility and safety, and did not affect normal organ functioning. Bi2S3-QD@DSPE hybrid clusters exhibited remarkable performance in CT angiography and fluorescence imaging in vivo.