The development of ideal contrast agents was of great importance for multimodal imaging. However, the simple combination of different contrast components always needed long-time preparation and a tough reaction environment. In this study, we introduced a one-step microwave-assisted approach to synthesize lysozyme-capped gold nanoclusters (Lys-Au NCs) rapidly instead of traditional conditions. Irradiation with continuous microwave power shortened the reaction time from several hours to one hour and generated a large red shift (50 nm) of the fluorescence emission. The ultrasmall Lys-Au NCs showed excellent properties, including high quantum yield (19.61%), good stability, low cytotoxicity and good biocompatibility. This eco-friendly nanoprobe provided significant contrast signals in both NIRF (near-infrared fluorescence) and CT (X-ray computed tomography) in vivo imaging. Further conjugation with folic acid made the nanoprobe favorable for targeted fluorescence imaging of cancer cells and tumor-bearing mice.