Land use changes from cropland to orchards in Eastern China have raised serious concerns about the regional nitrogen (N) cycle and greenhouse gas balance. We measured soil nitrous oxide (N2O) emissions and methane (CH4) uptake using manual static chambers in an apple orchard. The primary aims were to assess the effect of N fertilizer application on gas fluxes and quantify the site-specific N2O emission factor (EFd). Field experiments were arranged in a randomized block design with three N input rates (0, 800 and 2600/2000 kg N ha−1 year−1). We found that orchard soils were a negligible CH4 sink (−1.1 to −0.4 kg C ha−1 year−1). Annual N2O emissions responded positively to N input rates, ranging from 34.1 to 60.3 kg N ha−1 year−1. EFd ranged from 1.00% to 1.65% with a mean of 1.34%. The extremely large background emissions of N2O (34.1–34.3 kg N ha−1 year−1) most likely originated from nitrate accumulation in the soil profile because of historical overuse of N fertilizer. We conclude that (1) site-specific EFd is suitable for assessing regional direct N2O emissions from upland orchards; and (2) conventional fertilization regimes must be avoided, and reduced N input rates are recommended in the study region.