We selected 42 early-stage primary biliary cirrhosis (PBC) patients and 30 healthy controls (HC). Metagenomic sequencing of the 16S rRNA gene was used to characterize the fecal microbiome. UPLC-MS/MS assaying of small molecules was used to characterize the metabolomes of the serum, urine and feces. Liquid chip assaying of serum cytokines was used to characterize the immune profiles. The gut of PBC patients were depleted of some potentially beneficial bacteria, such as Acidobacteria,Lachnobacteriumsp.,Bacteroides eggerthiiandRuminococcus bromii, but were enriched in some bacterial taxa containing opportunistic pathogens, such as γ-Proteobacteria,Enterobacteriaceae, Neisseriaceae, Spirochaetaceae,Veillonella,Streptococcus,Klebsiella,Actinobacillus pleuropneumoniae,Anaeroglobus geminatus,Enterobacter asburiae,Haemophilus parainfluenzae,Megasphaera micronuciformisandParaprevotella clara. Several altered gut bacterial taxa exhibited potential interactions with PBC through their associations with altered metabolism, immunity and liver function indicators, such as those ofKlebsiellawith IL-2A andNeisseriaceaewith urinary indoleacrylate. Many gut bacteria, such as some members of Bacteroides, were altered in their associations with the immunity and metabolism of PBC patients, although their relative abundances were unchanged. Consequently, the gut microbiome is altered and may be critical for the onset or development of PBC by interacting with metabolism and immunity.