Ecological ditch–pond systems are important measures for controlling agricultural non-point source pollution, yet their practical application is constrained by unstable purification performance and large land occupancy. The effective application of such 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). Existing studies often fail to adequately capture the multi-level dynamic responses of water volume and water quality in such systems, which hinders their support for spatial layout optimization. Against this backdrop, 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 water depth in the paddy model was determined by inflows, outflows, and water consumption during each time step, while the total nitrogen and total phosphorus concentrations were simulated by considering fertilization, first-order pollutant decay, and inputs from rainfall and irrigation. For the ditch–pond unit model, water volume changes were governed by rainfall, evapotranspiration, seepage, upstream inflow, and drainage discharge. Pollutant concentrations in the ditch–pond unit model were calculated using two modes: static storage-based reduction and dynamic drainage-based reduction. The paddy and ditch–pond unit models were linked through system dynamics into an integrated field-ditch-pond system model, which 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 methodological reference for modeling multi-level wetland systems and offer a scientific basis for ecological control of agricultural non-point source pollution. Future work may further refine the simulation of water cycling and pollutant transformation processes within field-ditch-pond systems to enhance model accuracy and applicability.