Abstract: Ginseng (Panax ginseng) is a traditional Chinese medicinal herb that requires highly specific soil conditions for optimal cultivation. The growth and development of ginseng are often severely restricted by the high bulk density and low organic matter content in conventional farmland soils. Although molecular hydrogen (H₂) has been proven to promote plant growth and development, its gaseous form faces technical challenges such as poor storage stability and difficulties in field application. In this study, magnesium hydride (MgH₂) was innovatively incorporated into a microbial organic fertilizer. Using three-year-old ginseng plants as experimental materials, a large-scale field experiment was conducted to systematically investigate the effects of different application rates (0, 1.25, 2.5, and 5.0 kg·m⁻², designated as HD-CK, HD-1, HD-2, and HD-3, respectively) on ginseng agronomic traits, soil physicochemical properties, and enzyme activities. Our results showed that moderate application (HD-2 treatment, 2.5 kg·m⁻²) significantly promoted ginseng growth. The seedling survival rate was 89.11%, which was 12.87% higher than that of the control. At the wilting stage, the plant height, and leaf area increased by 40.87%, and 74.14%, respectively. At the red fruit period, chlorophyll content in HD-2 treatment increased by 15.12% than that of the control. In terms of soil fertility, the HD-3 treatment yielded the greatest improvements, with organic matter, total nitrogen, and total phosphorus contents increasing by 27.53%, 43.51%, and 38.20%, respectively, compared with those in the control. Under HD-3 treatment, soil enzyme activities were also significantly enhanced, the activities of soil sucrase, urease, amylase, acid phosphatase, catalase and cellulase during the green fruit stage increased by 322.73%, 42.36%, 63.87%, 12.00%, 30.03%, and 82.50%, respectively. Overall, the HD-2 treatment (2.5 kg·m⁻²) was identified as the most effective for promoting ginseng growth. The MgH₂–microbial organic fertilizer enhanced soil health and optimized microbial community structure through the synergistic effects of hydrogen, magnesium, and microorganisms, comprehensively improving soil physicochemical properties and enzyme activities, thereby promoting the growth and development of ginseng. Furthermore, the application of MgH₂–microbial organic fertilizer increased the relative abundance of beneficial soil microorganisms, enriched soil metabolic pathways, and reduced the abundance of the pathogenic fungus Fusarium spp., effectively promoting ginseng growth while lowering the risk of root rot disease. In this study, we provide an innovative technological pathway and theoretical basis for applying hydrogen in agricultural soil improvement, offering significant practical value for the green, efficient, and sustainable cultivation of valuable Chinese medicinal plants. Future research should focus on the dynamics of hydrogen release and its influence on the rhizosphere microbial community structure to facilitate the precise application and industrial development of this fertilizer.