The widespread use of antibiotics all over the world increases the risk of many metabolic diseases by altering the gut microbiota. Grape by‐products are of particular interest in the prevention of metabolic diseases, while only minimum amounts of these wastes are up‐graded or recycled at present. The study investigated the effect of grape pomace (GPE) and seed (GSE) polyphenol extracts on the recovery of gut microbiota after antibiotic cocktail treatment in high‐fat diet‐fed (HFD) mice. C57BL/6J mice were fed HFD together with antibiotic treatment by drinking water for 3 weeks. Then, GPE and GSE were supplemented for 7 days after withdrawal of antibiotics. The gut microbiota was characterized by a significant loss of diversity and certain important taxon after a 3‐week antibiotic cocktail treatment. The GPE and GSE supplementation during the restore period of gut microbiota had some positive effects. The relative abundance of gut microbiota was improved by GPE and GSE compared to the spontaneous recovery group. And gut microbiota diversity was also greatly changed by GPE and GSE, being indicated by the changes of Verrucomicrobia and Akkermansia in feces. These findings suggested that grape polyphenol extracts have a great influence on the recovery of gut microbiota after antibiotics and high‐fat diet treatment.