We proposed size-dependent microparticle filtration and particle trap by centrifugal force and mechanical restriction using three-dimensional magnetically driven microtool (3D-MMT) in a microfluidic chip. Novelties of this paper are summarized as follows. (1) Filtration of particles is robust against pressure fluctuation in microchannels rather than using only hydrodynamic force because particles are separated mechanically, (2) Clogging of the microparticles could be avoided by rotation of the 3D-MMT in a mcirochamber, (3) Size-classified microparticles can be trapped along the gaps in microchannels by flow control. Microparticles having different sizes flow in spiral microchannels and filtered according to their sizes by gaps between gaps and substrate by centrifugal force. Microparticles larger than the gap cannot pass through the gap and are kept flowing in the inner microchannel. Rotation of the 3D-MMT by magnetic force from an external magnetic circuit generates swirling flow in the microchamber. Size-classified microparticles can be trapped in microchannel by closing the drain port of the target particle. Trapped particles can be measured by direct observation and treated by reagent. After the experiment, trapped particles are extracted by open the drain ports. We successfully demonstrated microparticle filtration and microparticle trap of filtered particles in the developed microfluidic chip.