Jujube (Ziziphus jujuba Mill.) cultivation in arid regions of China faces severe soil constraints, including high alkalinity, low organic matter content, and poor water retention. Although soil amendments have demonstrated potential for improving soil quality, their combined effects on soil-plant-microbe interactions in desert agroecosystems remain poorly understood. This study conducted a three-year field experiment in a desert jujube orchard in southern Xinjiang, China, to evaluate six nitrogen fertilizer management strategies: urea alone (CK) or combined with biochar (NB), bentonite (NP), graphene (NS), biochar plus bentonite (NBP), or microbial inoculants (NW). Soil physicochemical properties, enzyme activities, bacterial community structure, and jujube yield were analyzed. Structural equation modeling (SEM) was employed to elucidate the pathways linking soil amendments to crop productivity. Results showed that NBP was the most effective in improving soil physical structure, significantly reducing bulk density and enhancing water retention capacity compared to the control. The NBP treatment also enhanced soil organic matter (30% increase), available phosphorus (119% increase), and urease activity (44% increase), resulting in the highest jujube yield (7.14 kg per tree). Bacterial community analysis revealed that NBP significantly increased Shannon diversity and enriched Actinobacteriota and Proteobacteria. SEM analysis indicated that urease activity served as a significant mechanistic pathway linking soil organic matter improvements to enhanced crop productivity. These findings demonstrate that combined application of biochar and bentonite with nitrogen fertilizer represents an effective strategy for improving soil quality, enhancing microbial functionality, and increasing crop yield in desert jujube orchards, providing a practical and synergistic amendment combination for sustainable soil management and productivity enhancement in arid agroecosystems.