The invention discloses a photoacoustic and fluorescence dual-mode integrated tomography imaging system and a photoacoustic and fluorescence dual-mode integrated tomography imaging method. The system comprises a modulation laser light source (1), a vibrating mirror (2), a sample rotary table (3), a filtering wheel (4), a gating intensified charge-coupled device (ICCD) camera (5), a photoacoustic detection acquisition module (6), a system control module (7), a computer (8), a data bus (9) and a control bus (10), wherein the vibrating mirror, the sample rotary table, the filtering wheel and the gating ICCD camera are positioned on the same straight line with the direction of lasers; the ultrasound transduction array normal direction of the photoacoustic detection acquisition module is perpendicular to the straight line to form a crossed vertical detection mode. According to the imaging method, light absorption distribution formed by photoacoustic tomography imaging is used as prior information for the reestablishment of fluorescence tomography imaging, and the positions of fluorophores, fluorescent yield and fluorescence lifetime parameters are reestablished by an iterative method. By the photoacoustic and fluorescence dual-mode integrated tomography imaging system and the photoacoustic and fluorescence dual-mode integrated tomography imaging method, the imaging complexity can be reduced, the cost of hardware can be saved, and the flexibility of the system and the reestablishing accuracy of the fluorescence tomography imaging can be improved.