Land use change (LUC) is a key factor affecting nutrient budgets in agricultural soils. Comparing the long-term trajectories of nutrient budgets and changes in soils at a regional scale with contrasting LUC is critical to optimizing nutrient management and minimizing adverse environmental effects. We investigated the nutrient budgets and changes in soils in two counties in the south Loess Plateau, China, with contrasting LUCs from 1992 to 2017. Wugong County has cereals as the main crop, whereas Meixian County has the main cereal crops changed to kiwi orchards. We found that nitrogen (N), phosphorus (P), and potassium (K) inputs in two counties increased rapidly, and the nutrient outputs by crop harvests remained relatively stable. This resulted in increasing nutrient surpluses in the soils of two counties. Nutrient surplus in the orchard-dominated county was higher than that of the cereal-dominated county, and nutrient use efficiencies were contrasting. High N surplus in the orchard-dominated county resulted in high nitrate-N accumulation in deeper soil profiles of orchards. High P and K surpluses in the two counties significantly increased available P and K in 0-20 cm depth. Soil available P and K in the orchard-dominated county were significantly higher than in the cereal-dominated county, which was also significantly higher than the threshold values of available P and K contents in soils. We conclude that comprehensive measures should be taken to control nutrient surpluses, which will help to balance nutrient inputs and outputs and minimize nutrient losses in intensive horticultural crop systems.