In order to explore the long-term and practical method of water and fertilizer conservation under soil conditions of greenhouse sandy land in Southern Xinjiang, three-year-old ‘Tunis’ soft-seed pomegranate was used as the test material, and three treatments were set up: no fruit tree hole storage brick (CK), fruit tree hole storage brick A (T1) and fruit tree hole storage brick B (T2). Soil physiochemical properties and the changes of pomegranate growth were measured from 2021 to 2022. The results showed that the application of two kinds of fruit tree hole storage bricks (T1, T2) significantly increased the contents of available phosphorus, available potassium, alkali-hydrolyzable nitrogen and total nitrogen in 20–40 cm soil layer in two years. In 2021 and 2022, the contents of available phosphorus increased by 23.64%, 26.13% and 18.85%, 13.90% respectively, the contents of available potassium increased by 7.56%, 8.57% and 4.91%, 5.29%, and the content of alkali-hydrolyzable nitrogen increased by 22.97%, 22.53% and 16.88%, 14.85%. Meanwhile, the application of two kinds of fruit tree storage bricks significantly increased the soil water content in 20–60 cm soil layer and significantly reduced the soil pH in 0–80 cm soil layer. Compared with CK, the growth of new shoots and petioles of pomegranate treated with T1 and T2 at 80 days after flowering increased significantly in 2021 and 2022. The length of new shoots increased by 27.30%, 29.21% and 31.84%, 25.37%, respectively. The thickness of new shoots increased by 17.25%, 9.25% and 16.03%, 13.74%, respectively. The petiole length increased by 0.78, 0.83 mm and 0.62, 0.51 mm, respectively. The petiole diameter increased by 0.44, 0.28 mm and 0.39, 0.27 mm respectively, and the overall effect of T1 was better. In summary, fruit tree hole storage bricks can promote the stable supply of soil nutrients in the sandy land of Southern Xinjiang, greatly increase soil moisture content while reducing soil alkalinity, and finally significantly promote the growth of greenhouse pomegranate, thus, can be used as a recommended technology for maintaining water and fertilizer in greenhouse fruit tree cultivation in Southern Xinjiang.