A surplus of nitrogen (N) fertilizer can reduce plant nitrogen use efficiency (NUE), however, biochar can improve nutrient uptake by altering soil properties and root growth. Therefore, the objective was to determine how biochar alter soil nitrate (NO3−-N) availability and root development, and then to affect the plant NUE. The biochar was prepared by heating the apple branches at 700 °C and low oxygen. The effects of biochar on NO3−-N leaching and nitrogen oxides fluxes in orchard soil treated with five biochar rates (0, 0.5%, 1%, 2% and 4%) were investigated, the nitrate reduction in the soil and roots, and the NUE of Hupeh Crabapple (Malus hupehensis Rehd.) were measured in two soils amended (or not) with biochar, at six N fertilizer rates, using the solution culture, amino benzene sulfonate and subtraction method, respectively. The results showed that 0.5–4% (w/w) biochar decreased the leaching ratio of NO3−-N (9.9–68.7%) and nitrogen oxides flux (6.3–19.2%) in the soil. Soil denitrification intensity were most significantly decreased in the presence of 1% biochar when N fertilizer was applied at 0–450 mg NO3−-N kg−1; the soil nitrate reductase (NR) activity decreased at the application of 0–50 mg NO3−-N kg−1 in the presence of biochar, The root NR activity and root activity of M. hupehensis were significantly increased in the presence of 1% biochar at the application of 0–300 mg NO3−-N kg−1. In the biochar-amended soil, when the highest root activity and NR activity were obtained, N fertilizer application rate were reduced by 33.3% and 66.7%, compared to the non-amended soil, respectively. The NUE of M. hupehensis was increased by biochar-amended from 6.77% to 261.53%, comparied with the non-amended soils. These results indicated that biochar amendment could decrease nitrate leaching and nitrate reduction in soil, and promote nitrate absorption and reduction by root, thereby increasing the biomass and NUE of M. hupehensis when the input of N fertilizer was reduced from 450 to 300 mg NO3−-N kg−1.