Abstract: Chalcopyrite often coexisted with molybdenite, and their flotation properties were similar, which made flotation separation difficult. Because of the magnetic differences between the two minerals, they could be separated by magnetic separation technology. The simulation model of high gradient magnetic separation of chalcopyrite and molybdenite was constructed, and the effects of magnetic field strength, pulsation frequency, and particle size on the separation of chalcopyrite−molybdenite were investigated. The experiment of pulsation high gradient magnetic separation of chalcopyrite and molybdenite was carried out. The simulation results indicated that there were significant differences in the motion trajectories of chalcopyrite and molybdenite in the magnetic field; chalcopyrite was captured by the magnetic medium under the influence of strong magnetic forces, while molybdenite was expelled from both sides of the magnetic medium by fluid resistance. Increasing magnetic induction intensity could improve the capture efficiency of fine chalcopyrite, but it inevitably increased the entrainment of molybdenite. Although the entrainment of molybdenite could be effectively reduced by increasing the pulsation frequency, the fine chalcopyrite would fall off from the surface of the magnetic medium more easily. The experimental results indicated that for an artificial mixed ore with a copper grade of 23.84% and a molybdenum grade of 10.31%, the pulsating high−gradient magnetic separation had achieved the best results under a magnetic induction intensity of 1.2T and a pulsation frequency of 200 r/min. The resulting copper concentrate had a copper grade of 32.74% and a copper recovery rate of 81.56%, while the molybdenum grade was 4.56% and the Mo recovery rate was only 13.48%. Among them, the recovery rate of coarse chalcopyrite (0.045~0.074 mm) was 44.56%, and that of very fine particles (−0.025 mm) was 12.98%, indicating that the magnetic medium had a better capture effect on coarse chalcopyrite. Addition, the residue of lime in the pulp will lead to a sharp decline in copper grade and recovery in the magnetic seprationsepration copper concentrate. The research findings will provide theoretical guidance and technical support for the high−gradient magnetic separation of chalcopyrite and molybdenite.