The influence of magnetic matrices, magnetic field intensity, secondary and three section superconducting magnetic separation on the separation was studied in this paper. The magnetic field and flow field characteristics of elliptic cross-section matrix were studied in the elliptic coordinate system. The motion equations of the magnetic particles were derived. The tests results show that molybdenum concentrate with Mo grade of 7.4% and recovery of 43.6%, copper concentrate with Cu grade of 33.0% and recovery of 93.5% could be obtained, which verified the feasibility of separating copper-molybdenum by superconducting magnetic separation.