Rural domestic sewage has become very serious, while only 17.4% of it is treated centrally or partially, which results in environmental pollution and waste of water resources. To solve this problem, a wastewater treatment system by modular coupling is proposed, and the processing module includes two or three of multi-stage ecological pond, multi-stage drop aeration ecological ditch and multi-stage drop dam. The analysis of three examples shows that the system has a good treatment effect on chemical oxygen demand (COD), total nitrogen (TN), ammonium nitrogen (NH₄⁺-N) and total phosphorus (TP), and the removal ratios are 90.22%, 82.07%, 91.60%, 81.48%, respectively, when the flow rate is 3 m³/h. After 28 days of continuous operation, the treatment capacity decreases by about 10%, indicating that the system has good long-term treatment performance. The removal ratio decreases slightly under different flow rates, which shows its great adaptability in different hydraulic conditions. In practical application, the system can select different coupling systems according to rural terrain and wastewater quality, and it is suitable for the treatment of rural domestic sewage and agricultural non-point source sewage and the repairment of urban sewage and lake eutrophic water body.