A novel microchip separation method for microparticles based on electromagnetophoresis was developed. In this method, a double Y-shape microchip with two inlets and two outlets was used for particle separation. Microparticles of two different sizes were suspended in an aqueous solution and introduced into the microchannel from one inlet with a stream of the aqueous solution without particles from another inlet by a hydrodynamic flow. Then, the particles with two different sizes were migrated orthogonal to the flow by elctromagnetophoresis and separated to different outlets based on the difference in their electromagnetophoric velocities, which depended on the size of particle. Using this method, at one outlet, 89% of 3 μm polystyrene latex particles were isolated from a mixture of 3 and 10 μm particles. By combining hydrodynamic focusing, both 3 and 10 μm particles were recovered at the different outlets with 100% purity and recovery, respectively. Even the separation of 3 and 6 μm particles was also achieved with about 98% recovery and purity. Moreover, yeast cells and polystyrene particles could be separated with high separation efficiency by this technique.