Microbial seed coating is an effective method to improve seed performance and alleviate salt stress. However, insufficient microbial survival rate and short storage period are the key factors limiting the use of microbial seed coating agents. In this study, we screened a growth-promoting functional strain from wheat rhizosphere. This strain was encapsulated within potassium alginate (A)/pectin (P) microcapsules to develop a microbial seed coating agent. The encapsulation process was optimized to achieve high efficiency, and the resulting microcapsules were evaluated for storage stability. Coated seeds were tested under salt stress (mild and severe) conditions to assess germination rates, biomass accumulation, root growth, chlorophyll content, antioxidant enzyme activities (superoxide dismutase, catalase, and peroxidase), oxidation markers (hydrogen peroxide and malondialdehyde), and plant hormones (auxin, gibberellin, abscisic acid, and cytokinin). Functional strain (Pseudoxanthomonas suwonensis) isolated from wheat rhizosphere have the ability to produce auxin, catalase and siderophores. The embedding rate of A/P microcapsules reached 79.67% after optimization. After 28 days of storage, compared with the control (uncoated bacteria), the survival rate of microcapsules was significantly increased by 27.96%. Under salt stress, compared with the blank control, A/P-coated seeds increased the germination rate (up to 18.33%), biomass and root growth. The chlorophyll content and activity levels of antioxidant enzymes (peroxidase, catalase, and superoxide dismutase) increased by 19.86–66.07%, 6.64–13.52%, 5.35–5.41%, and 2.28%, respectively. The contents of hydrogen peroxide and malondialdehyde decreased by 4.39% and 9.29–18.42%, respectively, the auxin, gibberellin, and cytokinin levels in wheat significantly increased by 8.06–9.68%, 8.32%, and 12.93–20.72%, respectively. This study demonstrates that A/P microcapsules effectively enhance the survival and functionality of P. suwonensis as a seed coating agent, significantly improving wheat's salt stress tolerance. The microencapsulated coating prolongs microbial viability during storage while promoting plant growth through biochemical mechanisms, providing an effective microbial coating carrier for crops under salt stress in agricultural production.