The mixed-cropping mode of hulless barley (Hordeum vulgare L) and peas (Pisum sativum L) can optimize the planting system, effectively enhancing crop nitrogen and phosphorus utilization and increasing yield. This mode has been widely applied in Qinghai Province, China. In this study, a split-plot experimental design was employed to investigate the bacterial and fungal communities in the rhizosphere soil of monocropping and mixed-cropping treatments under different fertilization levels. The Illumina MiSeq sequencing technology was used for the research, and the physicochemical properties of the soil were measured. The results indicated that with the increase in the application of nitrogen and phosphorus, the bacterial α-diversity in the rhizosphere of the mixed-cropping system initially increased and then decreased after reaching a peak. The α-diversity index of soil bacteria was higher under the mixed-cropping mode than under the monocropping mode. For the rhizosphere soil fungi in the mixed-cropping system, the Shannon index initially increased and then decreased, while the Chao1 and ACE indices decreased initially and then increased. Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Sphingomonas, and Pseudomonas comprised the predominant bacterial genera in the rhizosphere soil of the hulless barley–pea intercropping treatment, whereas Fusarium, Metarhizium, and Cladosporium dominated among the fungal genera across the 12 treatments. Under the same fertilization levels, the relative abundances of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium in the rhizosphere soil of the mixed-cropping treatment increased by 8.4 %, 7.1 %, 5.7 %, and 5.6 %, respectively, compared to the monoculture of hulless barley, with a decreasing trend as nitrogen and phosphorus levels increased. Compared to the monoculture of hulless barley, the relative abundance of Fusarium in the mixed-cropping treatment decreased by 37.3 %, 43.8 %, 56.8 %, and 40.3 %, respectively. Redundancy and correlation analyses suggested that the variation in bacterial and fungal diversity and community composition in the mixed-cropping zone due to the interaction between hulless barley and peas under different nitrogen and phosphorus fertilizer application levels was significantly correlated with changes in soil organic matter, available phosphorus, and alkaline hydrolyzable nitrogen.