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Exploring the interactive effect of water and fertilizer on yield, soil water and nitrate dynamics of young apple tree is of great importance to improve the management of irrigation and fertilization in the apple-growing region of semiarid northwest China. A two-year pot experiment was conducted in a mobile rainproof shelter of the water-saving irrigation experimental station in Northwest A&F University, and the investigation evaluated the response of soil water and fertilizer migration, crop water productivity (CWP), irrigation water use efficiency (IWUE), partial factor productivity (PFP) of young apple tree to different water and fertilizer regimes (four levels of soil water: 75%−85%, 65%−75%, 55%−65% and 45%−55% of field capacity, designated W₁, W₂, W₃ and W₄, respectively; three levels of N-P₂O₅-K₂O fertilizer, 30-30-10, 20-20-10 and 10-10-10 g plant^−1, designated F₁, F₂ and F₃, respectively). Results showed that F₁W₁, F₂W₁ and F₃W₁ had the highest average soil water content at 0~90 cm compared with the other treatments. When fertilizer level was fixed, the average soil water content was gradually increased with increasing irrigation amount. For W₁, W₂, W₃ and W₄, high levels of water content were mainly distributed at 50~80 cm, 40~70 cm, 30~50 cm and 10~30 cm, respectively. There was no significant difference in soil water content at all fertilizer treatments. However, F₁ and F₂ significantly increased soil nitrate-N content by 146.3%~246.4% and 75.3%~151.5% compared with F₃. The highest yield appeared at F₁W₁ treatment, but there was little difference between F₁W₁ and F₂W₂ treatment. F₂W₂ treatment decreased yield by 7.5%, but increased IWUE by 11.2% compared with F₁W₁ treatment. Meanwhile, the highest CWP appeared at F₂W₂ treatment in the two years. Thus, F₂W₂ treatment (soil moisture was controlled in 65−75% of field capacity, N-P₂O₅-K₂O were controlled at 20-20-10 g·tree^−1) reached the best water and fertilizer coupling mode and it was the optimum combinations of water and fertilizer saving.