Provided are a microscopic surgery system and a navigation method guided by optical coherence tomography. The microscopic surgery system may include: an object lens; a surgical microscope unit configured to perform two-dimensional imaging on an area to operate on via the object lens; an optical coherence tomography unit configured to perform two-dimensional tomography imaging on the area via the object lens, with an imaging field calibrated according to that of the surgical microscope unit; a processor configured to obtain navigation information based on the two-dimensional imaging by the surgical microscope unit and the two-dimensional tomography imaging by the optical coherence tomography unit, the navigation information comprising positional information of a body part to operate on and a surgical instrument for operating on the body part; and an output unit configured to output the navigation information to guide the surgical instrument to the body part.