Effects of secondary flow of the melt on the separation of inclusions from molten aluminum flowing in a square channel by a solenoid were investigated theoretically and experimentally. Numerical methods were used to calculate the secondary flow, the separation efficiency of inclusions, and the particle motion. It is found that there appear two recirculating loop flows in a quarter cross section of the channel and the separation efficiency of inclusions is significantly improved by the secondary flow mainly owing to the mixing effect. The separation efficiency increases with the increase of the effective magnetic flux density and the frequency of magnetic field, and decreases significantly with the increase of the size of the separator channel for a constant value of a/δ. However, it is possible to achieve high separation efficiency by using argesized square channels and high frequency magnetic field with the help of the mixing effect of secondary flow. The computed results of particle trajectories show that the secondary flow accelerates the transportation of the particles from the inner region to the vicinity of the wall and greatly shortens the separation time of those particles. The effects of secondary flow on the separation efficiency were confirmed by comparing the measured separation efficiency with the computed results.