A reasonable theory is proposed to explain the mechanism of the pulse phenomena in the intra cavity phase modulated all-fiber laser. Based on the self-pulsing theory in fiber laser and the spatial-coupling model in solid state laser, the physical mechanism of pulsed laser generation is investigated and explained. It is hypothesized that there are two perpendicular polarization models in the fiber laser, which are coupled with the spatial-coupling model as the solid state laser theory described. As the phase modulation induces timely change of phase difference between the two coupled perpendicular polarization models, the coupling of the two modes also changes and the pulsed laser is generated. Based on these two hypotheses, a mathematic model was established and qualitative investigation has been done. Simulative analysis a show that the theory agrees well with the experiments.