This study aims to optimize the current engineering system for drainage waterlogging and water environment in agricultural polder areas. The research object was taken as the Lixiahe polder area in Jiangsu Province, China. Therefore, a mathematical model was also proposed to determine the optimal water surface ratio in the ponds and drainage channels wetland system in study areas. The objective function was set as the present minimum of the total project cost. The constraint conditions mainly included the following relational expressions: 1) The relationship between the drainage capacity of the pumping station and the water surface ratio of ponds and drainage channels. 2) The optimal range of the maximum and minimum water surface ratio was determined in the study area, which was closely related to the local natural conditions, indigenous culture, and land planning. 3) The removal rates of TN, TP, and CODCr were selected to determine the relationships between water environmental capacity, ponds, and drainage channels wetland system in polder areas. The decision variables included the water surface ratio of ponds, the water surface ratio of drainage channels, and the design of drainage flow. An Intelligent -Genetic Algorithms (GAs) was utilized to solve the mathematical model, due to the nonlinear calculation rather than the general. After that, a case study was applied to the pond and drainage channel engineering system in the polder area of Funing County. The specific results were as follows: 1) The water surface ratio reached 11.35% under the open ditch drainage system in the planning areas, where the water surface ratio of ponds was 8.15%, particularly increased, compared with the current. 2) The water surface ratio of drainage channels reached 3.20%, which remained the current status. 3) The design drainage discharge was 41.01 m3/s, and the designed drainage modulus reached 0.86 m3/(s•km2). An optimization scheme was expected to fully meet the standard requirements of the regional 20-year flood drainage. At the same time, the water body quality inside the polder areas reached Class IV level, where the outside was Class V. Therefore, the adsorption and degradation of water to pollutants were enhanced to accelerate the removal rates of pollutants, with the increase of total water surface ratio. There were different proportions of water surface ratio between ponds and drainage channels, leading to the different removal rates of TN, TP, and CODCr, although the total water surface ratio was all the same in the polder areas. Correspondingly, the distribution of water surfaces dominated the interception and purification of pollutants by water bodies. This finding can also provide a strong reference for similar areas in flood control, drainage planning, reallocation of land, and river-lake water purification.