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China has the largest apple-growing area and fresh fruit production in the world; however, water shortages and low fertilizer utilization rates have restricted agricultural development. It is a major challenge to obtain scientific and reasonable irrigation and fertilization systems for young apple trees in semi-arid regions of northern China. A 2-year field bucket experiment with four irrigation levels of W1 (75–90% Fs, where Fs is the field water holding capacity), W2 (65–80% Fs), W3 (55–70% Fs), and W4 (45–60% Fs), and three fertilizer levels of F1 (27-9-9 g N-P2O5-K2O), F2 (18-9-9 g N-P2O5-K2O), and F3 (9-9-9 g N-P2O5-K2O) was conducted in 2019 and 2020, so as to explore the effects of different water and fertilizer treatments on the growth and physiological characteristics of young apple trees. The results showed that the plant growth, leaf area, and dry matter of young apple trees at each growing period reached maximum values under F1W2, and they showed a positive linear relationship with relative chlorophyll content (SPAD), net photosynthetic rate (Pn), transpiration rate (Tr), stomatal conductance (Gs), water consumption, and water use efficiency (WUE). With the growth of young apple trees, water-fertilizer coupling could significantly increase the leaf SPAD of young apple trees. Pn, Tr, and Gs reached the maximum value under F1W1, and although they decreased under F1W2, the water use efficiency increased by 2.3–25.7% and 4.0–23.8% under F1W2 compared with other treatments in two years, respectively. The water consumption of young apple trees increased with the increase of irrigation and fertilizer, and both dry matter and water productivity reached the maximum value under F1W2, which increased by 0.8%, 14.6% in 2019, and 0.6%, 11.1% in 2020 compared with F1W1, while water consumption decreased by 12.2% and 9.4% in both years. In conclusion, F1W2 treatment (soil moisture was controlled at 65–80% of field water holding capacity, and N-P2O5-K2O was controlled at 27-9-9 g) was the best coupling mode of water and fertilizer for young apple trees in semi-arid areas of northern China. [ABSTRACT FROM AUTHOR]