A field experiment was carried out in Fifteen-year-old ‘Gala’/M. hupehensis Rehd. trees with ¹⁵N and ¹³C labeled tracers, to understand the characteristics of absorption, utilization, distribution, loss of carbon and nitrogen nutrition and fruit yield and quality under different nitrogen application methods (ON, TN and IN represented traditional one-time nitrogen, topdressing nitrogen and infiltrating irrigation nitrogen application, respectively) during fruit developmental periods. The results showed that the ¹⁵N derived from fertilizer (Ndff) in each organ displayed an order of IN > TN > ON at the fruit maturity stage, and significant difference was observed in Ndff values among the newborn organs (fruit, leaf and biennial branches). The total N contents and ¹⁵N absorption amount were highest in IN and lowest in ON. Compared with ON, the ¹⁵N utilization rates in TN and IN were increased by 41.63% and 68.60% respectively, and the ¹⁵N loss rates were decreased by 10.60% and 18.63% respectively. The residue amount of ¹⁵N-urea varied across different treatments and soil layers, showing an order of IN > TN > ON in 0-40 cm soil layer, and an opposite pattern in 60-120 cm soil layer. The ratio of ¹³C partition in fruit and storage organs (perennial branch, trunk and coarse root) under TN and IN was significantly higher than ON, and the highest value in the vegetative organs (leaf and biennial branches) occurred in ON, and lowest in IN. In addition, the yield, fruit hardness, soluble sugar and sugar-acid ratio quality index reached the highest value in IN. Our findings indicated that infiltrating irrigation nitrogen application could decrease nitrogen loss, thus increasing the absorption and utilization of nitrogen significantly by trees, and then optimizing the distribution of photosynthetic products, which was the preferred form to the yield and quality of apple tree.