The invention discloses a method for controlling non-point source pollution of paddy field by integrating and combining trenches and ponds in the farmland, and relates to the technical field of agricultural environment protection. According to the invention, based on the coupling characteristics of water quantity and water quality of runoff of the paddy field, by combining the modern measurement technology, the information searching and transmission technology and the intelligent control technology, running-away control and circulation utilization of nitrogen and phosphorus runoff of the paddy field are achieved and objectives of reduction of nitrogen and phosphorus discharging, water body purification and resource recycling are achieved. The method is advantageous in that the self-cleaning function of the paddy field is developed; when the nitrogen and phosphorus concentration is higher than a threshold, outward discharging of the water on the field surface and in the pond is not performed or is reduced; stay time of the nitrogen and phosphorus in the paddy field is extended; and by use of initial rainfall runoff with the quite high contents of absorptive pollutants on the field face and in the pond, the runoff which is redundant later, cannot be absorptive and contains quite low pollutant contents is directly discharged through external discharging channels, so pollution to the surface water body by the rainfall runoff can be reduced to the greatest degree.