The invention discloses a device and a method for classifying microalgae in ship ballast water. The device comprises a micro-fluidic chip carrying platform, a micro-fluidic chip, direct current driving assemblies, an excitation light source, light filtering assemblies, light detection assemblies and data processing assemblies, wherein the micro-fluidic chip comprises a glass slide, a liquid storage hole A, a liquid storage hole B, a liquid storage hole C, a liquid storage hole D, a liquid storage hole E, a main channel, a first focusing channel, a second focusing channel, a detection channel, an impedance pulse sensing upstream detection channel and an impedance pulse sensing downstream detection channel. By using the micro-fluidic chip as a ship ballast water microalgae classification micro-platform, the device is convenient to carry and high in detection speed. Relevant photoelectric detection equipment can be in a small-size structural form and can be conveniently transported to the field. Therefore, compared with existing large classification equipment, the device has the advantages of small size, light weight, convenience in carrying and the like, and can be handheld for quick field classification.