Nutrient budget of farmland system is a driving force on the change of soil fertility. The spatial and temporal change of soil nutrient contents in recent years was studied on a regional scale in 6 experiment stations in Chinese Ecological Research Network. The results showed that the average content of soil organic carbon and total nitrogen increased except in Hailun and Changshu Experiment Station areas where the main soil is black soil and paddy soil. The possible reason is that C and N balance of the farmland system was unable to maintain the higher content of soil organic carbon and total nitrogen in the two kind of fertile soils. Soil average available P contents increased or decreased without a common temporal trend in 6 stations, but soil average available K contents mainly decreased except in Luancheng and Yingtan Experiment Station areas. The nutrient budget of farmland system decided the direction and extent of temporal change of soil nutrient contents. For soil available P and K, their annual change amount showed a significant positive relationship with annual budget of farmland system. However, such relationship did not exist for soil total N because the balance only considering the input from fertilization and nitrogen biofixing and the output from crop uptake are unable to express the real budget of N in farmland system. Also, the initial contents of soil organic carbon and total nitrogen affect their change direction, which will turn from increase to decrease when the initial content of soil organic carbon and total nitrogen is larger than 15.1 g/kg and 1.60 g/kg, respectively.