The invention discloses a navigation system and method of a minimally invasive surgery. The navigation system comprises a composite endoscope body, a spatial positioning device and a surgery navigation server. The method comprises the steps that preoperative diagnostic images are subjected to three-dimensional model reconstruction and preoperative planning before navigation is performed; during the navigation, three-dimensional optical image signals and two-dimensional ultrasonic image signals of intraoperative organs and tissue are simultaneously acquired and three-dimensional reconstruction is performed, a three-dimensional model of the preoperative diagnostic images with preoperative planning information is subjected to organ and tissue deformation correction, and a three-dimensional optical model and a dynamic preoperative registration model are subjected to registration and fusion, so that the functions of optical navigation and ultrasonic navigation are simultaneously achieved, the intraoperative optical navigation can be switched to the intraoperative ultrasonic navigation continuously in real time, and a key position point, an optimum surgical entry point and an internal travel path of the intraoperative organs and tissue are continuously achieved in all dimensions from surfaces of organs and tissue to inner structure of organs and tissue. The navigation system and method of the minimally invasive surgery overcomes the defect of relatively single and discontinuous functions existing in the prior art, and is capable of lowering surgical risks.