Techniques that can dexterously manipulate particles/cells are significant for biological detection, analytical chemistry, and material synthesis applications. Although there are many methods to realize the 3D manipulation in a static condition, there is a lack of sufficient 3D manipulating strategies in a continuous flow. We develop an integrated microsystem with a cooling system based on thermal convection to realize 3D manipulation in continuous flow. Theoretical modeling and experiments demonstrate that with increasing the temperature of a microheater, the moving direction of particles transfers from the y-axis to the z-axis. Based on the principle, focusing flow and single particles are manipulated in the y-axis and z-axis. Besides, five outlets in different z-axis are fabricated to demonstrate the application of particle sorting. This novel strategy offers a new direction for particle manipulation vertically and benefits to reveal the heat transfer in micro-scale, which can pave a path for generating the next integrated microfluidic system for particles/cells sorting. •3D manipulation for the fluid and particles based on thermal convection in the continuous flow was demonstrated.•A simulation model to predict thermal convection in the microchannel was developed.•3D Multioutlet sorting for single particles was developed.