Spheroids that are formed from aggregated cells enhance biological function compared to monolayer culture. In particular, hetero-spheroids composed of different types of cells, such as hepatocytes and endothelial cells, express tissue specific functions at a high level, which is advantageous for more precise drug screening and biological research. In this study, we propose rapid formation of three-dimensional hetero-spheroids consisting of hepatocytes and endothelial cells using micro-rotation flow. The hepatocytes are coated with collagen gel layers less than 200 nm thick to increase adhesion strength between hepatocytes and endothelial cells. Gel-coated hepatocytes and endothelial cells are collected in an array by micro-rotational flow and collagen-gel coating, thereby forming hetero-spheroids within 2 min. This array allowed the size of the three-dimensional spheroids to be hydrodynamically controlled by varying the cell density of the medium without altering the device geometry with standard deviations of less than 19%. The proposed microfulidic device, with its capacity of rapidly forming size-controlled hetero-cell aggregates, will offer an efficient experimental platform for heterospheroid study that will contribute to drug screening and regenerative medicine.