This paper describes a novel non-contact manipulation system using on-chip magnetically driven micro-tools (MMT). This system has sorting function of particles one by one with MMT. It has unique feature of installation of MMT directly in a microchannel which is unlike to the conventional cell sorter systems. The drive unit was remarkably downsized by using an amplification mechanism of magnetic power actuated by electromagnets. We have demonstrated sorting of micro-beads automatically based on trigger signals generated by real-time image recognition. The proposed method can be extended to the environmental particulate analysis, cell sorting system and so on.