Background Gut microbiota is considered as an important endocrine organ and has remarkable influence on the metabolic phenotype of host, with extensive participation in the cometabolism with host. Significant changes occurred in intestinal microenvironment of cirrhotic patients under the influence of gut-liver axis. Hepatic encephalopathy is one of the common complications of cirrhosis. Methods In this study, four patients of cirrhosis accompanied with hepatic encephalopathy (CHE) were enrolled, with their healthy relatives as the controls, and paired comparison analysis was carried out. Fresh fecal samples were collected from participants, and subjected to Illumina MiSeq high throughput sequencing of 16S rRNA regions, and metabolome analysis was carried out using high-performance liquid phase chromatography and gas chromatography coupled with tandem mass spectrometry (HPLC-GC/MS-MS). Results Both the intestinal microbiota community and metabolome analysis showed distinct differences between CHE patients and the normal. CHE patients contained a remarkably decreased abundance of Bacteroidetes, whereas increased abundances of Firmicutes and Proteobacteria compared with the normal. Metabolome analysis revealed significant changes in metabolites constituents for CHE patients, showing distinct higher concentrations of amine, alanine, glutamic acid, ornithine, and tyrosine, with lower concentrations of cholesterol, myo-inositol, serine, suggesting the metabolic balance of intestinal microbiota was disrupted. The initial equilibrium state of gut microbiota community and metabolism was broken due to CHE. Conclusions Our study illustrated the intestinal microenvironment dysbiosis and dysfunction characteristics, which will be expected to provide guiding significance for intestinal microecological therapy and improvement of patients prognosis clinically.