The invention relates a magnetic particle control system positioning a magnetic particle (or magnetic particles) at a specific area, and more particular, to a magnetic particle control system including at least two magnets apart from each other, wherein a magnetic particle is positioned at a specific area between the at least two magnets by a repulsive force between the magnets. According to the exemplary embodiment of the invention, the magnetic particle can be consistently positioned at a wanted area by the at least two magnets with the same poles facing each other. Accordingly, the magnetic particle can be effectively controlled by arbitrarily adjusting the position of the magnets.