Diarrhea, caused by porcine epidemic diarrhea virus (PEDV), is a catastrophic gastrointestinal disease among suckling piglets, with high infectivity, morbidity, and mortality, causing huge economic losses to the pig industry. In the present study, we investigated the different microbiota from the cecal mucosa and cecal contents between healthy and PEDV-infected piglets. High-throughput 16S rRNA gene sequencing was performed to explore differences. The results revealed that microbial dysbiosis by PEDV infection occurred in the cecal mucosa and contents of suckling piglets at each microbial taxonomic level. The abundance of pathogenic bacteria associated with diseases, including diarrhea, was increased. The abundance of Fusobacterium was 26.71% and 33.91% in cecal mucosa and contents of PEDV-infected group, respectively, whereas that in the healthy groups was 17.85% and 9.88%. The proportion of Proteobacteria in the infected groups was relatively high (24.67% and 22.79%, respectively), whereas that in the healthy group was 13.13% and 11.34% in the cecal mucosa and contents, respectively. Additionally, the proportion of Bacteroidetes in the healthy group (29.89%, 37.32%) was approximately twice that of the PEDV-infected group (15.50%, 15.39%). "Nitrate reduction", "Human pathogens diarrhea", "Human pathogens gastroenteritis", "Nitrite respiration", and "Nitrite ammonification" were the enriched functional annotation terms in the PEDV-infected groups. Porcine epidemic diarrhea virus infection increased the proportion of harmful bacteria and decreased the proportion of beneficial bacteria in the cecal mucosa and contents of suckling piglets. Our findings suggest that determining the intestinal microbiota might provide a promising method to prevent PEDV and open a new avenue for future research.