The invention discloses a method for treating rural rivers through multi-stage ecological pond. According to the method, the multi-stage ecological pond comprise multi-stage ecological pond systems, each ecological pond system is arranged on the two sides of one rural river, and is arranged at intervals in the flow direction of the corresponding rural river and comprises ecological ponds, overflowdams and water gates, each ecological pond is a semi-circular flow channel, the two ends of each ecological pond are communicated with the corresponding rural river, aquatic plants are planted all around in each ecological pond, an aerating device is arranged in each ecological pond, meanwhile, fishes are bred in each ecological pond, and each overflow dam is located in the corresponding rural river and is used for forcing river water to flow into the corresponding ecological pond. The method for treating the rural rivers through the multi-stage ecological pond systems fully relies on an ecological treatment technology and has the advantages of being low in construction and maintenance cost, good in treatment effect, free of secondary pollution, simple in later-period operation management, capable of beautifying the landscape and the like; and in addition, the problem of rural river pollution can be solved, and the water quality problem caused by the fact that the rural rivers flow toa downstream main stream can be effectively solved.