The invention discloses an endoscope-based multispectral video navigation system and method. The system comprises an endoscope head module used for internal inspection, a light source module used for providing near infrared and visible light sources, an optical signal acquisition module used for acquiring near infrared and visible light images, a multispectral conversion module used for imaging different spectrum segments, and a controlling and processing module used for controlling a camera and processing the acquired images to achieve video navigation. The invention also discloses a method utilizing the system to achieve multispectral video navigation. By adopting the system and the method, the problem that at present, most endoscope fluorescent products can only see fluorescent images or visible light images but not multispectral images is solved, technical monopoly of foreign companies in China is broken through, the imaging research threshold of the multispectral endoscope is lowered, the selection space of optical molecular imaging probes is expanded, and the optical molecular imaging research and application ranges are extended.