Magnetic chromatography is an effective system for fine magnetic particle separation because of its strong magnetic field gradients. We have been developing the magnetic chromatography system to separate two or more kinds of fine magnetic particle with different sizes. To evaluate the performances of our developed system, we have also developed a simulation code with taking into account the fluid dynamics and magnetics. It is, however, difficult to consider two or more kinds of fine magnetic particles with different sizes in the simulation, because magnetic interferences between two or more kinds of magnetic particles need to be considered. Therefore, we have newly developed a simulation code to deal with magnetic interferences between two or more kinds of fine magnetic particles.