We have numerically investigated the motion of an elliptical magnetic particle in a microfluidic channel subjected to an external uniform magnetic field. By using the direct numerical simulation method and an arbitrary Lagrangian–Eulerian technique, the involved particle–fluid-magnetic field problem can be solved in a fully coupled manner. The numerical predictions of the particle trajectory and orientation with and without a uniform magnetic field are in qualitative agreement with the existing experimental results, and numerical results have revealed the impacts of key parameters such as inlet flow velocity, magnetic field direction, and particle shape on the rotational motion and lateral migration of the elliptical particle. Meanwhile, the shape-based particle separation in a low Reynolds number flow with the aid of an applied uniform magnetic field has also been numerically demonstrated.