ABSTRACTEndometritis is a common cow disease characterized by inflammation of endometrium, which leads to infertility or low fertility of cows and brings huge economic losses to the dairy industry. Tau interferon (IFN-τ) has many important biological functions, including an anti-inflammatory effect. The present study aimed to survey the effects of IFN-τ administration on gut microflora and body metabolism in mice with endometritis and to explore the potential relationship. The results indicated that IFN-τ obviously alleviated the damage and ultrastructural changes of mouse endometrium induced byEscherichia coliand enhanced tight junction protein’s expression level. Through analysis by 16S rRNA gene sequencing, we found that IFN-τ, especially at 12 h, could regulate the composition of gut microbiota associated withPediococcus,Staphylococcus, andEnterorhabdusinE. coli-induced mouse endometritis. Through histometabonomics, it was found that endometritis was related to 11 different metabolites and 4 potential metabolic pathways. These metabolites and metabolic pathways were major participants in metabolic pathways, cysteine and methionine metabolism, arachidonic acid metabolism, and pyrimidine metabolism. Correlation analysis of gut microbiota with uterine tissue metabolomics showed that changes in metabolic pathways might be affected by gut microbiota, such asEnterorhabdusin mouse endometritis. The above results indicated that the anti-inflammatory mechanism of IFN-τ might be reduction of the abundance ofEnterorhabdusin the gut microbiota, affecting the expression level of important metabolites in uterine tissue and thus playing an anti-inflammatory role.IMPORTANCEThe change in intestinal flora has been the focus of many disease studies in recent years, but the pathogenetic effect of interferon on endometritis is still unclear. The results of this study showed that IFN-τ alleviated the damage in mouse endometritis induced byE. coliand improved the endometrial tissue barrier. Its functional mechanism may be reduction of the abundance ofEnterorhabdusin the intestinal microbiota, affecting the expression level of important metabolites in uterine tissue and thus playing an anti-inflammatory role.