In order to solve the problems of nitrogen (N) losses and fruit quality degradation caused by excessive N fertilizer application, different dosages of the nitrification inhibitor, 3,4dimethylpyrazole phosphate (DMPP) (0, 0.5, 1, 2, and 4 mg kg −1 soil), were applied during the later stage of 'Red Fuji' apple (Malus domestica Borkh.) fruit expansion in 2017 and 2018. The effects of DMPP on soil N transformation, carbon (C)-N nutrition of tree, and fruit quality were investigated. Results revealed that DMPP decreased the abundance of ammonia-oxidizing bacteria (AOB) amoA gene, increased the retention of NH 4 +-N, and decreased NO 3 −-N concentration and its vertical migration in soil. DMPP reduced 15 N loss rates and increased 15 N residual and recovery rates compared to the control. 13 C and 15 N double isotope labeling results revealed that DMPP reduced the capacity of 15 N absorption and regulation in fruits, decreased 15 N accumulation in fruits and whole plant, and increased the distribution of 13 C from vegetative organs to fruits. DMPP increased fruit anthocyanin and soluble sugar contents, and had no significant effect on fruit yield. The comprehensive analysis revealed that the application of 1 mg DMPP kg −1 soil during the later stage of fruit expansion effectively reduced losses due to N and alleviated quality degradation caused by excessive N fertilizer application.