Since 1990s, dramatic land-use changes have occurred across mainland China. Large areas of cereal lands have been converted into horticultural crops because of lucrative economic benefits. Fruits and vegetables together in China have consumed more than 30% of N fertilizers. Therefore, understanding the long-term effects of land use change from cereals to orchard on N budgets in croplands at the county scale over long-term is very important for managing N in agricultural systems in China. We selected three Counties (Luochuan (LC), Mixian (MX), and Wugong (WG)) on the Loess Plateau with different land-use changes since 1990s in Shaanxi to compare the changes of N budgets in croplands at the county scales. The main crops in the three Counties were cereals (wheat and corn) before 1990s. After 1990s, the land uses in LC and MX changed dramatically; and LC and MX become the main apple and kiwifruit production county in China, respectively. The main crops in WG are still wheat and corn. It provides an ideal reference to compare the effects of land use changes on N budgets in croplands at the county scale. The N inputs and outputs, N surplus and N use efficiency (NUE, computed as N in harvested crop products divided by N inputs) at the three Counties from 1990 to 2017 were quantified. The annual N inputs and N surplus of the three Counties since 1990s were increased, and NUE decreased significantly. Compared to WG, the annual N input and N surplus of cropland of LC and MX were very high, and NUE was very low. For example, NUE in LC decreased from 64% in 1990 to 12% in 2017; and NUE in WG decreased from 55% in 1992 to 38% in 2017. To understand the fate of surplus N in cropland of LC, we also collected soil profile samples (0-6 m) from cereal lands and apple orchards in different sites of the county. The average nitrate accumulation in 0–6 m soil profiles reached 5611 kg N/ha in 2017. Approximately 67% of the total N surpluses in LC from 1990 to 2017 was accumulated in soil profile as nitrate. Land use change from cereals to orchard result in high surplus N in croplands at the county scale. The nitrate accumulation in the vadose zone is the main fate of surplus N in the intensive agricultural landscape, which should be considered an important component of the soil N budget to optimize production and environmental protection.