Pulsating high-gradient magnetic separation (PHGMS) is a promising method of separating chalcopyrite from other minerals with similar floatability. However, the capture characteristics of chalcopyrite in the PHGMS process remain poorly understood. In this study, the difference in the capture capacity of chalcopyrite and hematite, a typical weak magnetic mineral, was theoretically compared. The effects of the key operating parameters, i.e., magnetic induction, slurry flow rate, and magnetic wire diameter, on the capture difference between chalcopyrite and hematite, were investigated through experimental verification. The comparison results showed that chalcopyrite shared a similar capture trend with hematite. The capture mass weight of the matrix decreased with an increase in the pulsating frequency, slurry flow rate, and magnetic wire diameter, but it increased with improved magnetic induction. However, chalcopyrite exhibited a smaller capture mass weight due to its lower susceptibility, which required a higher magnetic induction (1.4 T), slower flow rate (1.5 cm/s), lower pulsating frequency (150 rpm), and smaller matrix diameter (1 mm) for higher efficient recovery of chalcopyrite. As the magnetic induction increased from 0.8 T to 1.6 T, the chalcopyrite recovery improved from 65.84% to 75.80%. These findings provide valuable information for improving the utilization of chalcopyrite.