Abstract: In China, the control of Spartina alterniflora in a chemical way is in its initial stage, and the effects of chemical drugs on ecosystems during use are not well understood. In order to provide a scientific basis for using imazapyr to remove S. alterniflora, we investigated the temporal dynamics of soil microbial communities in the experimental plot (sprayed with 25% imazapyr aqueous solution, 17.91 L/hm²) and the control plot (not sprayed with the imazapyr). The results showed that there was no significant difference in soil microbial diversity between the experimental plot and the control plot, but there were significant differences in soil microbial diversity at different times under the same treatment. Imazapyr only affected the relative abundance of a samll group of microbes (e.g., Actinobacteriota, Zygomycota, etc.). In the first 6 days after spraying imazapyr, the bacterial community structure changed greatly, but the imazapyr had no significant effect on fungal community structure. There was no significant difference between experimental plot and control plot in the proportion of metabolic pathways of bacterial community, but there was a significant difference in the proportion of metabolic pathways of fungal community. The proportion of common significant difference metabolic pathways of bacteria in the experimental plot and the control plot had a similar trend with time changing, while fungi were the opposite. In conclusion, imazapyr had little effect on soil microbial diversity, and it mainly affected the bacterial community structure ranther than fungal community structure, while fungal community function was more affected by imazapyr than the bacterial community.