Irradiation flux is an important parameter to the material irradiation damage investigation, for space material irradiation damage evaluation and the accelerated ground-based test, the irradiation flux effects cannot be ignored. In this paper, the polyimide was set as the research object, the irradiation flux effect and mechanism are investigated by the means of electron paramagnetic resonance test, and based on the free radical dynamic analysis, the dynamics mode of free radical population in vacumm can be established as a function of irradiation time (or proton irradiation flux). The results show that the free radical anneal process in vacuum follows the exponential mode, and the characteristic time constant τradical-vacuum is about 1.9h. Furthermore, a simplified method is proposed with the investigation of the free radical behavior of the irradiated surface modification polyimide (TiO2/PI), and the characteristic time constant τbulk is 1.9h, which is almost the same to the value of τradical-vacuum.