A two-year field trial was conducted in order to assess techniques to control ginger blast and explore the effects of fumigants on soil bacterial microorganisms and ginger metabolites. This study examined the effects of dazomet and chloropicrin on the control of ginger blast and their influence on ginger yield in Luoping County, Yunnan Province, China. The results showed that in 2022, the control effectiveness of dazomet and chloropicrin treatments on ginger blast was 84.33% and 94.67%, respectively. The corresponding yields were 50,154.40 kg/hm2 and 50,296.90 kg/hm2. In 2023, the control effectiveness of dazomet and chloropicrin treatments on ginger blast were 86.33% and 93.67%, respectively, and the yields were 65,115.83 kg/hm2 and 65,337.93 kg/hm2. In both years, the incidence of ginger blast in the control group reached nearly 100%, leading to the near extinction of the crop. Additionally, in 2023, 16S rRNA high-throughput sequencing and non-targeted metabolomics techniques were used to analyze the effects of the fumigants on soil bacterial microorganisms and the metabolites in ginger. The results showed that the diversity and richness of soil bacterial communities were lower than those in the control group at 0 and 120 days after treatment with two fumigants, but the relative abundances of beneficial bacteria such as Pseudomonas increased at 60 days, and the relative abundances of Actinobacteria, Gemmatimonadetes, and Bacillus increased at 120 days. The abundance of Firmicutes also increased after 120 days of chloropicrin treatment. The non-targeted metabolic LC–MS results showed that the production of phenols and terpenoids was upregulated after dazomet and chloropicrin treatments. The contents of amino acids and their derivatives were also upregulated. This upregulation of metabolites was beneficial to the flavor quality of ginger and enhanced its anti-inflammatory, anti-tumoral, and antioxidant effects.