Abstract: To greatly shorten study period, reduce cost and obtain systematic and completed results when studying the influence of management zone size on variable-rate fertilization, the simulation system, integrating geographical information system (GIS) with computer simulation and model based management system, was designed and developed for simulating the influence of management zone size on variable-rate fertilization. The system is composed of data management, model management, simulation analysis and decision analysis. On the basis of the minimum scale soil nutrient distribution generated randomly based on the given values of mean, standard deviation and related distance, or obtained by geostatistics analysis based on soil sampling data, the amount of fertilization, yield and fertilization use efficiency at different scales were calculated by related fertilizer models and yield models supported by geographical information system (GIS) and computer simulation, then the simulation result was intuitively visualized by curve graphics and RGB primitive colors synthesized image and thematic maps. Result shows that the spatial analysis and visualization technologies of GIS and the computer simulation technology will provide effective tools to process and analyze data and visualize the results for the study on variable-rate fertilization.