Abstract: Soil fumigants are widely used to protect agricultural and high-value cash crops from soil-borne diseases. As broad-spectrum agents, however, fumigants also have side effects on non-target organisms. Dimethyl disulfide (DMDS) is a new alternative to methyl bromide (MeBr) that reduces plant fungal pathogens and nematodes. DMDS is therefore recommended by the Methyl Bromide Technical Options Committee of the United Nations Environment Program (UNEP). This study was an attempt to identify the effects of DMDS on microbial communities in protectorate soils under continuous cropping. The efficacy of DMDS was evaluated by bio-assay in the laboratory. The efficacy of DMDS on the Fusarium spp. and Phytophthora spp. was observed after fumigations. The LC₅₀ of DMDS with different concentrations (170.00 mg·kg^-1, 85.20 mg·kg^-1, 42.50 mg·kg^-1, 21.30 mg·kg^-1 and 10.62 mg·kg^-1) was 42.08 mg·kg^-1 and 115.15 mg·kg^-1, respectively to Fusarium spp. and Phytophthora spp. Microbial community structures after DMDS fumigation were evaluated using BIOLOG Ecoplates under laboratory conditions. Compared with the untreated/control plants, the average well color development (AWCD) of the DMDS 10.62 mg·kg^-1, 42.50 mg·kg^-1 and 170.00 mg·kg^-1 respectively increased by 8.46%, 6.02% and 19.31%, 0 day after fumigation and 120 h after sample incubation. AWCD increased by 1.87%, 3.47% and 8.01%, respectively, 240 h after incubation; which indicated that DMDS promoted the growth of microbes. AWCD of treated samples were close to the control at 14 days after fumigation. The indices of Shannon and Simpson at 0 day after fumigation were higher than that of the control, recovering to the levels of the control 7 days after fumigation. Based on McIntosh index, there was no significant difference between the fumigation treatments and the control. Principal component analysis of substrate reaction reflected that the use of carbon sources by microbial community was obviously different in the treatments immediately after fumigation. It was, however, close to the control 14 days after fumigation. The study showed that DMDS fumigation promoted microbial activity, and affected the carbon sources consumption of microbe. However, effects became very weak and the indicators recovered to the levels of the control treatment at 14 days after fumigation. It indicated that DMDS fumigation not only effectively controlled soil-borne pathogen spread, but was also environmentally safe. The study laid the basis for a scientifically-guided use of fumigants.