A second near-infrared window/first near-infrared window dual-mode fluorescence tomography system having a lighting module, an excitation module, a second near-infrared window collection module, a first near-infrared window collection module, a CT imaging module and a central control module. The central control module is configured to reconstruct second near-infrared window three-dimensional and tomographic images and first near-infrared window three-dimensional and tomographic images based on the white light images, the second near-infrared window fluorescent images, the first near-infrared window fluorescent images, and the CT images. The reconstructed three-dimensional space tumor signal has depth characteristics, which is closer to the real distribution of tumors, such that the reconstruction position is more accurate. The three-dimensional shape of the tumor is displayed intuitively and clearly at any angle with the usage of image display unit.