The present invention provides an in vivo photon analysis system and method, wherein the system comprises: an in vivo device and an in vitro device； the in vivo device comprises: an intervention function module which enters into a human body, outputs a laser output by the in vitro device to a preset position, and acquires a feedback fluorescence of the preset position； the in vitro device comprises: a laser light source module which outputs a first group of laser and a second group of laser； a coupling and switching module which couples the first group of laser to obtain a first to-be-output laser, couples the second group of laser to obtain a second to-be-output laser, acquires the feedback fluorescence, and sends the feedback fluorescence to an analyzing and testing module； an analyzing and testing module which receives the feedback fluorescence, and analyzes the feedback fluorescence, so as to obtain analysis results of the feedback fluorescence, and send the analysis results of the feedback fluorescence to a core processing module； and a core processing module which controls the laser light source module to output the first group of laser, and controls the laser light source module to output the second group of laser according to the analysis results of the feedback fluorescence.
