To comprehensively understand anaerobic degradation of the novel cis-nitromethylene neonicotinoid insecticide Paichongding (IPP) and its impacts on microbial communities in anaerobic soils, we investigated IPP degradation characteristics, kinetics, and pathway in four different soils. The bacterial community in response to the application of IPP using pyrosequencing of 16S rRNA gene amplicons was also studied. The removal ratio of IPP stereoisomers (RR-IPP, SS-IPP, RS-IPP, and SR-IPP) reached >90% at 60 days after IPP treatment (DAT) in yellow loam soil (F) and paddy field on desalting muddy polder (C), whereas the degradation ratios of RR-IPP and SS-IPP were <30% at 60 DAT in Huangshi soil (J) and yellow paddy soil (H). The results showed that the anaerobic degradation rate of IPP and its stereoisomers was strongly affected by soil physical-chemical characteristics. Furthermore, on the basis of the six metabolites (M1-M6) identified by LC-MS/MS and their behavior, the anaerobic degradation pathway of IPP in soils was proposed. Biodegradation of IPP involved continuous biocatalytic reactions such as nitro reduction and elimination, hydrolysis, demethyl, and ether cleavage reactions. A higher richness of operational taxonomic units (OTUs) was found in soils without IPP application than in soils with IPP application. Both the rarefaction curves and Shannon-Wiener diversity index in anaerobic soils had significant difference after IPP application, and the community composition also differed at both the phyla and genus levels.