The present invention relates to a method of separating fine particles by measuring the magnetic susceptibilities thereof using isomagnetophoresis. In a system for separating fine particles using isomagnetophoresis according to the present invention, fluids having different magnetic susceptibilities and fine particles to be measured are introduced into a microfluidic channel to form a magnetic susceptibility gradient, a strong magnetic field is applied to the channel to control the behavior of the introduced fine particles, thus moving the fine particles to respective positions at which the fluids having magnetic susceptibilities identical to those thereof is present. According to the present invention, fine particles having a fine difference in magnetic susceptibility can be separated from each other by measuring the magnetic susceptibilities thereof.