Polyvinyl chloride microplastics (PVC MPs) have attracted a lot of attention regarding their potential environmental and health risks. However, their effects on the microbial interaction in anammox process are still unclear. In this study, the long-term effects of different concentrations of PVC MPs (i.e., 0, 1, 15, 50 mg/L) on anammox process were investigated. The results showed that only high concentration of PVC MPs (50 mg/L) induced the performance fluctuation of nitrogen removal but it quickly returned to normal. The rise of the PVC MPs concentration led to a gradual decrease in the particle size of the sludge granules and an increase in the Proteins (PN)/polysaccharides (PS) ratio in extracellular polymeric substances (EPS). PVC MPs significantly reduced the microbial diversity and altered the overall microbial community structure. Network analysis showed that low concentration of PVC MPs (1 mg/L) could increase the network size and complexity, while high concentration of PVC MPs (50 mg/L) reduced the network complexity as the number of nodes and links decreased significantly (P < 0.05). Also, 50 mg/L PVC MPs promoted the communication efficiency among the microbial network in terms of the low path distances, which might be the strategy of microbial community to resist the external environment perturbation and further maintain the system performance stability. Similar trend was found in the subnetwork of Planctomycetota, an important phylum of anaerobic ammonium oxidizing bacteria (AnAOB). This study enriches our understanding of the response of microbial interaction among anammox microorganisms under the stress of PVC MPs.