In order to explore the accurate management mode of water and fertilizer supply for young apple tree in semi-arid region, the bucket cultivation experiment was conducted to study the response mechanism of physiological properties and crop water productivity of two-year-old young apple tree to different water and fertilizer treatments. The treatments consisted of four irrigation levels: 75%~85% (W1), 65%~75% (W2), 55%~65% (W3) and 45%~55% (W4) of field capacity, and three fertilization (N—P2O5—K2O) levels: 0.6—0.6—0.2 (F1), 0.4—0.4—0.2 (F2) and 0.2—0.2—0.2g/kg (F3) water-free soil. The results showed that relative and saturated water contents and SPAD value of young apple trees’ leaves all can reflect the deficit status of soil moisture. The highest and lowest proline were found in F1W4 and F3W1 treatments (that in F1W4 was increased by 440.8% compared with F3W1), and the highest and lowest malonaldehyde were found in F3W4 and F1W1 treatments (that in F3W4 was increased by 167% compared with F1W1), respectively. The highest water use efficiency of leaf (WUE) and crop water productivity (CWP) both appeared in the treatment of F2W2 of which the net photosynthetic rate Pn, transpiration rate Tr and stomatal conductance Gs were decreased by 18.8%, 29.1% and 23.2%, respectively, while WUE was increased by 14.2%, dry mass was decreased by 5.2%, water consumption was also decreased by 16.4% and CWP was increased by 13.4%. WUE can reflect the CWP to some degree and the treatment of F2W2 reached the best water and fertilizer coupling mode.