The invention belongs to the technical field of biomedical laparoscope, and particularly relates to a 3D optical molecular imaging laparoscopic imaging system, aiming at solving the problem in existing laparoscope technology and fluorescent laparoscopes. The system comprises a 3D laparoscope, wherein two output optical channels of the 3D laparoscope are parallel; a dual-channel charge coupled device (CCD) is respectively arranged outside the 3D laparoscope corresponding to two eye lenses, and a beam splitter prism is arranged in each dual-channel CCD; a cut-off filter is arranged at the near infrared channel behind the beam splitter prism, and a black-white near infrared CCD is arranged behind the cut-off filter; and a colored CCD is arranged at the visible light channel behind the beam splitter prism. According to the 3D optical molecular imaging laparoscopic imaging system, a target optical molecular image is precisely integrated with a visible light image, and is displayed in a 3D manner, so that the 3D structure of a target focus and the 3D anatomical relationship of the 3D structure and surrounding tissues can be displayed precisely, rich deep information is provided to doctors, and the accuracy of doctor operation and scientific researches can be greatly improved.