The invention discloses a high-throughput screening method of duckweed. The method comprises the steps of 1, acquiring initial images of duckweed of different strains; 2, intercepting a single duckweed image according to the initial images to obtain the intercepted image; 3, processing the intercepted image to obtain the initial area of the duckweed; 4, repeating steps 2 and step 3 to obtain initial area of the duckweed of different strains from a porous plate culture device; 5, transferring the porous plate culture device and duckweed into a culture box to culture for a period of time under the same culture condition, and then acquiring a duckweed image; 6, repeating steps 2 to 4 to acquire the area data of the duckweed of different strains after culturing for a period of time; 7, acquiring the area increasing rate of the duckweed of different strains according to the initial area, the area after culturing for a period of time, and the culture time. With the adoption of the method, destructive sampling can be avoided during screening the duckweed, and moreover the workload of screening the duckweed can be reduced.