Jujubes (Ziziphus jujuba) are a crucial industry in the arid region of Xinjiang, facing challenges such as water scarcity and low water use efficiency. This study focuses on jujube orchards located at the edge of the Taklimakan Desert to investigate whether applying trace elements can effectively enhance jujube growth, development, and fruit quality. By foliar spraying boron and zinc micro-fertilizers onto jujube leaves, we analyzed the effects of different doses on growth parameters, photosynthetic activity, crop yield, water use efficiency, and fruit quality. The results revealed that the length of the fruit branch, leaf area index, and fruit longitudinal/transverse diameter increased by 19.35%, 25.72%, and 32.9%/2.28%, respectively; net photosynthetic rate, transpiration rate, and stomatal conductance increased by 105.51%, 91.43%, and 75.3%, respectively, while intercellular CO2 concentration decreased by 13.09%; yield and water use efficiency improved by 16.95% and 12.68%, respectively; soluble sugar content, titratable acid content, and flavonoid content increased by 13.56%, 51.63%, and 86.12%, respectively. Based on these findings, the optimal application rate for boron micro-fertilizer was determined to be 3.51~3.59 kg/hm2, and for zinc micro-fertilizer, it was 3.16~3.32 kg/hm2. This study provides practical methods along with theoretical support for applying micro-fertilizers in arid regions.