Crops are often subjected to low survival rates in saline-alkali soil, due to the saline-alkali stress. The increasing number or variety of functional microorganisms in the saline-alkali soil can be expected to significantly promote the growth of plants. In this study, the microbial community structure of saline-alkali soil was analyzed to isolate the functional microorganisms with the growth-promoting using high-throughput sequencing. A multifunctional composite microbial agent was constructed to mix the existing antagonistic bacteria with the isolated growth-promoting bacteria. A systematic investigation was made to clarify the growth-promoting on the mung beans under saline-alkali stress. Two strains were identified by molecular biology. The phosphorus and potassium solubilization of strain SI-1-3 were verified by culture media. The Salkowski colorimetric technique was used to determine the production of the IAA (indole-3-acetic acid) product. Spectrophotometry was used to identify the secretion of GA (gibberellin). The inhibitory capability of antagonistic Y-2 against pathogenic bacteria was determined using the petri dish confrontation. The compatibility experiment among strains was conducted for the composite microbial formulation in a petri dish using the cross-line method. The saline-alkali conditions of the tested soil in the pot experiment were determined to measure the saline-alkali tolerance range of the composite microbial agent. Pot experiments were used to clarify the effects of compound strains on the emergence rate, incidence rate, growth indicators, and physiological and biochemical indicators of mung beans. The growth promotion was verified for the composite microbial agent. The results showed that Proteobacteria, Actinobacteria, and Firmicutes were the dominant bacterial communities in the soil samples, while Ascomycota shared the highest proportion of fungal communities. A bacterium named SI-1-3 was isolated with a higher isolation frequency from the dominant strains. It was identified as Bacillus subtilis, with the ability to dissolve organic phosphorus, decompose potassium elements, and secrete indole-3-acetic acid and gibberellin. According to the phylogenetic tree, the antagonistic strain Y-2 was Pichia membranifaciens. Plate experiments showed that antagonistic bacterium Y-2 shared a significant inhibitory effect on Fusarium raminearum and Pyricularia oryzae Cav. There was no antagonistic effect between the two strains through compatibility tests. They were co-cultured to construct a composite microbial formulation with a volume ratio of 1:1. The saline-alkali tolerance of the composite bacterial agent was identified to determine the best growth of the strain in the PDB medium. Therefore, a pH value of 8.5 and NaCl concentration of 5% were selected as the saline-alkali stress conditions for the subsequent experiments. The mung beans were then planted in the saline-alkali soil with the composite microbial agent. There was a certain promoting effect of composite microbial agent on the growth of mung beans under saline-alkali stress conditions with pH 8.5 and NaCl concentration of 5%. The emergence rate of mung bean increased by 7.44% in the pot experiment, whereas, the incidence rate decreased by 82.37%, compared with the control group. Additionally, the root length, plant height, and fresh weight of stem and leaf that were treated by the composite microbial agent increased by 75.24%, 64.33%, and 66.67%, respectively. At the same time, the chlorophyll, soluble sugar, and soluble protein content of mung bean seedlings increased by 71.63%, 64.21%, and 77.87%, respectively. There was the promoting effect of composite microbial agents on the plants. Thus, the finding can provide an effective microbial resource to improve the saline-alkali land and agricultural development.