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.