We have developed a system that can separate planktons and other microorganisms in a liquid according to their characteristics based on the electromagnetophoresis and microfluidic control. Rapid growth of planktons causes public health problems such as red tides and damage to the fishing industry, so a compact system that can immediately inspect the state of planktons on the spot is very effective in solving this problem. In this study, we developed a system that can separate microorganisms such as fine-grained phytoplankton by combining electromagnetophoresis, which occurs when a magnetic field and electric current are applied orthogonally to each other, and a microfluidic device, utilizing the phenomenon in which electromagnetophoresis force increases with particle size. The system is capable of characterizing microorganisms by measuring their migration distance and speed through image analysis. Using the developed system, we have demonstrated the possibility of highly efficient separation of microorganisms based on the migration distance and speed of each size particle in the range of 10 to 50 μm in diameter.