Magnetic separation is a very useful tool in medicine manufacturing, sludge disposal and we have developed the magnetic chromatography system, which separates the magnetic particles or the ions from fluid due to its strong magnetic field gradients in the very small flow channel. There are many fine ferromagnetic wires on the wall of the developed magnetic column. A superconducting magnet applies a strong magnetic field to the magnetic column, and fine ferromagnetic wires make strong magnetic field gradients. It was, however, impossible to accurately evaluate the performance of the developed magnetic column due to the absence of a good simulation method. In order to enhance the accuracy of the simulation it is necessary to couple the fluid dynamics simulation with the magnetic field simulation. Therefore, we have developed a simulation code dealing with the fluid dynamics, solving Navier-Stokes, control volume, and magnetic field equations simultaneously, and compared the simulation result with the experimental one to verify the validity.