The invention discloses a multiplayer overflowing type ecological cleaning pond applicable to a farmland drainage ditch. The multiplayer overflowing type ecological cleaning pond comprises a purifying pool body, two water inlet troughs, purification grooves, water separation walls, purification boxes, a gate, water pumps and water inlet pipes, wherein the purifying pool body is communicated with the farmland drainage ditch and is separated into the two water inlet troughs and a plurality of purification grooves with different depths through the water separation walls, and the purification boxes are arranged in the purification grooves. The purification grooves have a graded cascade structure, agricultural wastewater enters the water inlet trough after passing through the water pumps and the water inlet pipes and then flows through the purification grooves step by step under the action of a pressure head, and purified water finally flows back into the farmland drainage ditch. The efficient volume fraction of the cleaning pond can be improved, the hydraulic retention time of sewage in the pond is prolonged, the content of eutrophic substances in farmland drainage can be effectively lowered, and non-point source pollution in farmland is prevented from expanding to the outside. The multiplayer overflowing type ecological cleaning pond has the advantages of small floor space, high purification efficiency, simplicity in manufacture and convenience in maintenance, and an original water-logging drainage function of the farmland drainage ditch is not influenced.