Developing effective regulatory strategies to enhance irrigation water and fertilizer efficiency in the southern Xinjiang region of China, while simultaneously combatting desertification, is of paramount significance. This study focuses on Chinese jujube in Xinjiang and presents findings from a two-year field experiment aimed at investigating the optimal application strategy of microbial organic fertilizer (MOF). The research aims to provide a scientific foundation for achieving high-quality jujube production. The experiment involved a control group (utilizing only freshwater, referred to as CK) and various combinations of MOF treatments. In 2021, these treatments included M1 (0.6 t/ha), M2 (1.2 t/ha), M3 (1.8 t/ha), and M4 (2.4 t/ha), while in 2022, they encompassed M1 (0.6 t/ha), M2 (1.2 t/ha), M4 (2.4 t/ha), and M5 (4.8 t/ha). Over the two-year trial period, we assessed various indices, including the soil’s physical properties, hydraulic characteristics, soil enzyme activities, and relative chlorophyll content. Additionally, we evaluated jujube yield, quality, and economic benefits. The results indicate that MOF application led to significant improvements in soil conditions. Specifically, the average moisture content and profile water storage of the 0–50 cm soil layer increased by 10.98% to 36.42% and 1.8% to 26.8%, respectively. Moreover, in both the 2021 and 2022 experiments, soil saturated water content (SSWC) and water-holding capacity (WHC) increased by 6.25% to 15.98%, while soil hydraulic conductivity (Ks) and bulk density (BD) decreased by 2.91% to 9.88% and 0.63% to 8.08%, respectively. In 2021, MOF application resulted in significant enhancements in soil enzyme activities, with urease activity increasing by approximately 22.5% to 100.5%, peroxidase activity rising by around 24.2% to 148.5%, and invertase activity augmenting by about 5.4% to 32.9%. Notably, the M4 treatment in 2021 demonstrated a substantial jujube yield increase of approximately 19.22%, elevating from 7.65 t/ha to 9.12 t/ha. Based on comprehensive analysis, this study recommends an optimal MOF application rate of approximately 2.4 t/ha. This approach not only provides robust support for the sustainable development of the jujube industry but also serves as a valuable reference for enhancing local soil resilience against desertification.