In the southern Xinjiang region of China, developing efficient irrigation and fertilization strategies to enhance resource utilization and prevent desertification is of critical importance. This study focuses on jujubes in Xinjiang, China, and involves a three-year field experiment aimed at exploring the optimal application strategy of magnetically treated water combined with microbial organic fertilizer to provide scientific support for high-quality jujube production. The experiment included a control group (using only fresh water, denoted as CK) and combinations of magnetically treated water drip irrigation with varying amounts of microbial organic fertilizer: in 2021, treatments included M0 (only irrigating with magnetically treated water), M6 (0.6 t/ha), M12 (1.2 t/ha), M18 (1.8 t/ha), and M24 (2.4 t/ha); in 2022 and 2023, treatments included M0, M6 (0.6 t/ha), M12 (1.2 t/ha), M24 (2.4 t/ha), and M48 (4.8 t/ha). This study investigated the effects of magnetically treated water drip irrigation combined with microbial organic fertilizer on soil physical properties, hydraulic parameters, enzyme activity, aggregate stability, and jujube yield and quality. The application of microbial organic fertilizer significantly reduced the soil bulk density by 3.07% to 11.04% and increased soil porosity by 1.97% to 14.75%. Soil saturated hydraulic conductivity gradually decreased with the increasing amount of microbial organic fertilizer, with a reduction range of 5.95% to 13.69%, while the water-holding capacity significantly improved (from 0.217 cm3/cm3 to 0.264 cm3/cm3). Additionally, microbial organic fertilizer significantly enhanced the activities of urease, catalase, and sucrase in the soil and significantly increased the proportion of large soil aggregates. Jujube yield increased by 3.66% to 21.38%, and the quality significantly improved, as evidenced by the increase in soluble sugar and flavonoid content. The Gauss model calculation results recommended 3.09 t·hm2 as the optimal amount of microbial organic fertilizer for comprehensively improving jujube yield and quality. These findings indicate that magnetically treated water drip irrigation combined with high amounts of microbial organic fertilizer significantly improved soil physical properties, hydraulic parameters, enzyme activity, aggregate stability, and jujube yield and quality, providing scientific evidence for desert soil improvement and agricultural production.