Traditional Chinese medicine targeted at gut microbiota has good effects in relieving the clinical manifestation of Alzheimer's disease, and intestinal metabolites are considered as a bridge of communication between the brain-gut axis. In order to explore the molecular mechanism of Ganmaidazao decoction treatment, first, the model rats induced by Aβ25-35 and d-gal were used to test the therapy of Ganmaidazao extract using the Morris Water Maze, Western Blot and Elisa. Then the 16S rDNA gene sequencing of the gut microbiota as well as UPLC-QTOF/MS-based metabolomic analysis of feces were carried out. Last, the relationship between Alzheimer's disease, gut microbiota and metabolites was analyzed. Results showed that the abundance and diversity of gut microbiota were rescued and the changes of fecal metabolites in rats with Alzheimer's disease were reversed after Ganmaidazao decoction administration, which were mainly related to lipid metabolism, steroid hormone metabolism, energy metabolism, amino acid metabolism and bile acid metabolism. After associating with Spearman’s correlation analysis, we concluded that gut microbiota and metabolites were closely related and Ganmaidazao decoction could interfere with the balance of gut microbiota and their corresponding metabolites to exert anti- Alzheimer’s disease effect. Combined with PICRUSt2 functional prediction of gut microbiota and metabolomics results, phenylalanine metabolism has been focused as a key metabolic pathway, and Ganmaidazao decoction can reduce the abnormal accumulation of phenylalanine and phenylpyruvate and promote their metabolism by restoring the activity of phenylalanine hydroxylase. This integrated omics approach has potential roles in understanding the complex mechanisms of Ganmaidazao decoction in treating Alzheimer’s disease.