In the development history of high gradient magnetic separation (HGMS), the introduction of pulsating flow was extremely important, it successfully solved the problem of matrix clogging and allowed continuous and stable operation in the industry. However, the current pulsating HGMS (PHGMS) theory remains inadequately understood. In this paper, a 2D simulation model was established in COMSOL Multiphysics to reveal the magnetic field characteristics, flow field distribution, and particle capture dynamics in a PHGMS system. Quantitative comparisons were carried out between single-wire and multi-wire systems in the presence and absence of pulsation flow. The simulation results indicated that due to the coupled effect of neighboring magnetic wires in matrix, the magnetic field strength around an individual magnetic wire would slightly drop while the flow field velocity would increase. The introduction of pulsating flow could increase the peak value of fluid velocity and give particles a chance to move up and down. The analysis of particles travels length and capture probability indicated that the recovery for fine particles might be improved by increasing the strength of pulsating flow. This study provided a novel strategy for the highly efficient recovery of fine, weakly magnetic materials.