Microfluidic combined with magnetic field have been demonstrated to be the promising solutions for fast and low-damage particles separation. However, the difficulties in the precise layout of magnets and accurate prediction of particle trajectories lead to under and over separation of target particles. A novel particle separation lab-on-chip (LOC) prototype integrated with microstructures and micropolar arrays is designed and characterized. Meanwhile, a numerical model for the separation of magnetic particles by the synergistic effect of geometry-induced hydrodynamics and magnetic field is constructed. The effect of geometry and magnetic field layout on particle deflection is systematically analyzed to implement accurate prediction of particle trajectories. It is found that the separation efficiency of magnetic particles increased from 50.2% to 91.7% and decreased from 88.6% to 85.7% in the range of depth factors from 15 µm to 27 µm and width factors from 30 µm to 60 µm, respectively. In particular, the combined effect of the offset distance of permanent magnets and the distance from the main flow channel exhibits a significant difference from the conventional perception. Finally, the developed LOC prototype was generalized for extension to arbitrary systems. This work provides a new insight and robust method for the microfluidic separation of magnetic particles.