The system frame work and operation mechanism for ArcIMS were analyzed. Based on the platform of ArcIMS 9.0, a scheme with multi architecture for WebGIS was put forward with the help of ASP.NET technology. Combined with the knowledge models of farmland nutrient balance and environmental risk assessment, the WebGIS-based information system for the nutrient balances and environmental risk evaluation in Chinese agroecosystem has been developed. The system included six function modules named as basic database management module, data query and analysis module, the nutrient thematic mapping module, on-line nutrient analysis module, environmental risk assessment module, and fertilizer consultancy service module. Combining map data with the result of the modules which deal with agricultural basic data, the system could provide the services of on-line share, evaluation and consultation of the national farmland nutrient balance and environmental risk assessment.