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.