Abstract: To explore the causes of repeated outbreaks of diarrhea in a pig farm in Sichuan. Utilizing next-generation sequencing technology (NGS), combined with conventional PCR and sequencing methods to test and verify the piglet′s enteric intestinal samples. The results show the presence of porcine epidemic diarrhea virus (PEDV) exists in this farm. The PEDV strain was found to be a separate branch through phylogenetic tree analysis of the PEDV S1 gene. The porcine circovirus type 3 (PCV3) was also detected in the disease samples. This indicates that the diarrhea problem in the farm may be due to the co-infection of the new PEDV strain and the PCV3 strain.