This paper is based on nutrient budget and its effects on soil nutrient status in typical greenhouse system in China to provide a basis for raising the utilization rate of fertilizers and maintaining the sustainable development of agriculture in the greenhouse. By investigating the management of 18 representative greenhouses in Shouguang, Shandong Province, China, and analyzing both the greenhouse and open field soil samples, the soil nutrient budget and the trend of nutrient accumulation and translocation in soils were thus studied. The results under greenhouse system showed that the average annual inputs of N, P 2O 5 and K 2O were 4 088, 3 655 and 3 437 kg ha −1, respectively. The total inputs of N, P 2O 5 and K 2O provided by chemical fertilizers which are the main source of soil nutrient were 63, 61 and 66%, respectively. The utilization rates of N, P 2O 5 and K 2O were only 24, 8, 46% and the input ratio among N, P 2O 5 and K 2O (1:0.9:0.8) was quite different from the uptake ratio (1:0.3:1.4). It had caused the excess of N, P 2O 5 and K 2O in the soil, and the theoretical surpluses were 3 214, 3 401 and 2 322 kg ha −1, respectively, for N, P 2O 5 and K 2O. The level of the organic matter, total nitrogen, nitrate nitrogen, available phosphorus, and available potassium was increased substantially, and their maximum level was observed in the topsoil (0–20 cm) with an average value being 1.4, 1.9, 21.2, 5.4, and 3.7 times higher than that of the open field soil, respectively. The greenhouse soils showed leaching of the nutrients, especially NO 3 − which would cause a potential risk to the quality of groundwater in the area. It is necessary to apply more organic manure and provide nutrients according to the crop requirements and soil fertility as it could not only produce high crop yield, but also be beneficial to balance the soil nutrient and improve the utilization rate of fertilizers. Further, there would be no significant surplus of nutrients which may leach out of soil to contaminate the environment.