Under the long-term stress of chlorimuron-ethyl, the diversity and evenness of soil microbial community decreased, and more importantly, some bacterial and fungal species that possibly benefited soybean's growth, e.g., Acidobacteria, γ-proteobacteria, Cortinarius violaceu, Acarospora smaragdula, and Xerocomus chrysenteron decreased or demised, while some species that could induce the obstacle of soybean's continuous cropping, e.g., Fusarium oxysporum, Rhizoctonia solani, and Phytophthora sojae, increased or appeared. Some actinomycetes were inhibited having negative effects on the antagonism between soil microbes. It is considered that due to the longer half-life of chlorimuron-ethyl in soil and the resistance and resilience of soil microbes to short-term environmental stress, long-term in situ investigation rather than laboratory microcosm test or short-term field experiment would be more appropriate to the accurate assessment of the ecological risk of long-term chlorimuron-ethyl application. Further studies should be made on the application mode and duration of chlorimuron-ethyl to reduce the possible ecological risk of applying this herbicide on continuously cropped soybean field.