Abstract: The study of regional symbiosis ecosystem with the regulation of food chain material flow as the core is an important research content in the field of sustainable development. Based on the material flow analysis method and system dynamics modeling platform, evaluation framework for nitrogen flow effect in regional food chain was constructed. Nitrogen flow in regional food chain was analyzed and simulated in Qingpu district of Shanghai. The results indicate that: (1) From 2000 to 2014, the input and output of food chain nitrogen experienced a sharp decline to gradually stable process without regional self-sufficient in nitrogen products. (2) Under the baseline scenario, the negative effects of nitrogen flow in food chain on environment are generally small, but the agricultural production capacity in 2020 can not meet the demand of local population for nitrogen in meat and aquatic products. (3)Under the optimized scenario, the input of fertilizer nitrogen was reduced by 53.75%, and the agricultural production met the consumption needs of the local resident population. The amount of nitrogen products in outside region was reduced by 2 245.16 t, the comprehensive nitrogen cycle efficiency was increased to 25.54%, and the impact of agricultural production on water environment was reduced. The optimized scheme not only guarantees food security, but also protects the environment from the impact of intensive agricultural production. The research results can provide methods and ideas for nitrogen nutrient management in regional food chain.