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Paddy field drainage discharged directly into natural waters without the treatment will aggravate water eutrophication. The removal characteristics of the purified paddy field drainage was explored by establishing an experimental device that simulates a compound ecological ditch (CED), which significantly optimized the absorption capacity of nutrients in rice fields. The results show that the changes of pollutants before and after the experiment indicates that the CED has a significant effect on the removal of pollutants in the drainage of the paddy field. The degradation trend of pollutants in 5 rice growth cycles is in agreement with the first-order kinetic degradation model. Bio-phase microscopy and microbial diversity index reveal that the species of bacteria and plankton algae increase in the continuous operation of the CED, accompanied by the emergence of higher micro-animals. It shows that improved ecosystem water quality is more suitable for the survival and reproduction of various microorganisms. The research results provided a new idea for further improving paddy field drainage treatment efficiency.