Tongzhouwan port area is a new port area of Nantong port to be developed along the coast of Nantong，which is of great significance for alleviating the contradiction between port and city along the Yangtze River and implementing the regional integration development strategy of the Yangtze River Delta. Based on the natural resource conditions and the distribution of environmentally sensitive areas near the planning region，we put forward the optimized and adjusted planning scheme of the Tongzhouwan port area from the environmental impact concern. Applying the mathematical model，analytic hierarchy process，and other methods，we compare the optimized scheme and the original scheme from the perspectives of resource occupation，hydrodynamic condition，water environment capacity，and ecological environmental impact. The results show that the optimized scheme better balances port development and ecological environment protection. The research result may serve as a reference for the coastal ecological port planning.