To probe into the flow and aggregation behaviors of thermo-responsive microspheres in microchannel during the phase transition. the flow, characteristics of monodisperse poly(n-isopropylacrylamide) (PNIPAM) microspheres in microchannel with local heating are investigated systematically. When the fluid temperature in the microchannel increases across the lower critical solution temperature (LCST), the PNIPAM microspheres finish the phase transition within 10 s and are easily get aggregated during the phase transition. The diameter ratio of microsphere to microchannel, number of microspheres, initial distance between microspheres, and flow direction of fluid in microchannel, are key parameters affecting the flow and aggregation behaviors of the microspheres in microchannel during the phase transition. If a proper combination of these parameters is designed, the microspheres can aggregate together during the phase transition and stop automatically at a desired position in the microchannel by local heating, which is what the targeting drug delivery system expected. (C) 2009 American Institute of Chemical Engineers AIChE J. 55: 1559-1568, 2009