In this study, the authors use GIS to simulate the influence of management zone size on variable-rate fertilization in soil with different soil nitrate levels. Field distribution dataset series of soil nitrate concentration in 500m×500m field were generated based on given mean, standard deviation and related distance. Each dataset is composed of nitrate concentration values at 10⁴ cells, each being 5m×5m in size. The amount of fertilizer used and yield of field unit from scale 100 to 1 were then calculated based on the generated soil nitrate distribution. The results show that when the size of a management zone decreases, precise fertilization will increase or maintain, instead of decreasing, the fertilization rate, and yield and nitrogen use efficiency will also increase. As the size of a management zone has much influence on reasonability for variant rate fertilization and yield in fertilization critical nutrient transitional areas, spatial variation becomes less and the scale effect on variable rate fertilization less significant when soil fertility is higher.