In this study, a novel system based on magnetophoretic chips has been designed and simulated for the manipulation and controlled size-based separation of magnetic microparticles within a microfluidic environment. The system consists of magnetic nanofilms in the form of interconnected disks with a separation gap and a rotating magnetic field generated by permanent magnets. The magnetic field generator setup, using a stepper motor and an Arduino controller, enables adjustment of the rotation frequency. Three-dimensional modeling was carried out using SolidWorks, and the distribution of the magnetic energy on the chip was simulated using COMSOL Multiphysics. Additionally, particle trajectories and magnetic forces were analyzed through custom-developed MATLAB codes. The simulation results, for validation purposes, were compared with experimental data from previous studies, and the good agreement of the particle trajectories (with an average radial error of 2.61%) demonstrated the high accuracy of the simulations. Then, using this validated model, the performance of the designed system in particle separation was evaluated, and it was found that by selecting gaps of 2 to 7 micrometers, under magnetic field strengths of 50 and 100 Oersted and by adjusting the frequency, micrometric particles with different sizes could be separated. By eliminating challenges associated with coil circuits and undesired heating in previous methods, this study provides a reliable, simple, and efficient solution with biological and medical applications.