China is rich in magnetite mineral resources, but they are generally characterized by low grade, fine dissemination size, and a high content of harmful impurities. Wet low-intensity magnetic separation (WLIMS) is an important method for processing fine-grained magnetite. However, during the separation process, fine magnetite particles are prone to magnetic agglomeration, which makes it difficult for conventional WLIMS separators to achieve high-selectivity separation. To address this issue, a novel WLIMS separator based on a rotating magnetic system was developed in this investigation, and its separation characteristics were systematically investigated through a combined approach comprising CFD–DEM–FEM multiphysics coupling simulations and experimental validation. Simulation results indicate that the rotating magnetic system significantly reduces the chain length and the structural stability of magnetic agglomerates just as magnetite particles enter the magnetic field region. Furthermore, under the rotating action of the magnetic system, the magnetic chains only enclose a portion of the intergrowth minerals, while gangue minerals remain unattached, which positively contributes to improved separation selectivity. Both laboratory-scale experimental results and industrial production data indicate that, compared to the conventional WLIMS separator, the rotating magnetic system WLIMS separator achieves significantly superior separation performance. For a magnetite ore with a grade of 57.68%, the rotating magnetic system WLIMS separator achieved an optimal concentrate grade of 65.43% (with a recovery of 94.78%), whereas the conventional WLIMS separator attained only 60.32% at a similar recovery rate. This investigation provides an important basis for the large-scale industrial application of rotating magnetic system WLIMS separators and the efficient development and utilization of fine-grained magnetite resources.