As a widely used fungicide, the environmental fate of carbendazim and its residues in agricultural products have caused great concern. However, its effects on soil microbial communities are largely unknown. Herein, we used high-throughput sequencing to reveal the effects of high and low dose of carbendazim and its degrading strain, Rhodococcus qingshengii strain djl-6, on the composition, diversity, and interrelationship of soil bacterial and fungal communities in short- and medium-term under laboratory conditions. The results showed that carbendazim exhibited an increased negative impact on bacterial communities and reduced the proportion of dominant fungal phylum Ascomycota during a 14-day incubation period. Only the impacts of low-dose carbendazim (2 mg·kg dry soil) on fungal community were weakened. Network analysis showed that carbendazim increased the connectivity and modularity of microbial co-occurrence networks. Strain djl-6 exhibited good potential for bioremediation of carbendazim-contaminated soils. Moreover, it driven the assembly of potential carbendazim-degrading consortia from indigenous microbial communities; and members of the genera Arthrobacter, Bacillus, Brevundimonas, Lysinibacillus, Massilia, Mycobacterium, Paenibacillus, and Pseudarthrobacter might be participated in the degradation of carbendazim. Taken together, our study provides a relatively comprehensive understanding of the effects of carbendazim and its degrading strain djl-6 on soil microbial communities.