Abstract: The effective application of ecological ditch-pond systems in irrigation districts depends not only on the design and operation management of individual units, but also significantly on their spatial layout (including system area and unit connection pattern). Given that existing studies often fail to adequately capture the multi-level dynamic responses of water volume and water quality in such systems, thereby limiting their support for spatial layout optimization, this study proposes a system dynamics-based simulation method for optimizing the spatial layout of ditch-pond systems in irrigation districts. A field-ditch-pond system model was developed using the system dynamics simulation tool Vensim, integrating water balance, pollutant removal processes, and hydraulic connections among ditches and ponds. The model was calibrated and validated using field monitoring data. A case study was conducted in a typical double-cropping paddy high-standard farmland demonstration area in southern China. The model verification results show that the developed model can effectively simulate the dynamic variations of water volume and pollutant concentrations in the system. The case analysis results show that: 1) With increasing ditch-pond to paddy area ratio, nitrogen and phosphorus removal rates rise, but the rate of increase gradually slows down, suggesting an optimal range of 5%～9%; 2) During the late rice season or under larger area ratios, concentrating wetlands in a single drainage path results in a significantly lower removal rate compared to other layouts; 3) For practical implementation, it is recommended to first determine an appropriate area ratio based on target pollutant reduction goals. Subsequently, wetlands may be placed either at the main drainage outlet or distributed in parallel across different drainage pathways, depending on site-specific conditions. The findings provide a scientific basis for ecological control of agricultural non-point source pollution.