Obesity is a serious health problem, and it is important to discover natural active ingredients for alleviating it. In this study, we investigated the effect of phenolamide extract (PAE) from apricot bee pollen on obese mice fed a high-fat diet (HFD). The main compounds in PAE were identified by HPLC-ESI-QTOF-MS/MS, and HFD-fed mice were treated with PAE for 12 weeks. The results demonstrated that the content of phenolamides in PAE was 87.75 ± 5.37%, with tri-p-coumaroyl spermidine as the dominant compound. PAE intervention in HFD-fed mice effectively reduced weight gain and lipid accumulation in the liver and epididymal fat, increased glucose tolerance, reduced insulin resistance and improved lipid metabolism. In terms of the gut microbiota, PAE could reverse the increase in the Firmicutes/Bacteroidetes ratio in HFD-fed mice. In addition, PAE could increase beneficial bacteria such as Muribaculaceae and Parabacteroides, and reduce harmful bacteria such as Peptostreptococcaceae and Romboutsia. Metabolomic analysis revealed that PAE could regulate the levels of metabolites, including bile acids, phosphatidyl choline (PC), lysophosphatidylcholine (lysoPC), lysophosphatidylethanolamine (lysoPE) and tyrosine. This is the first study finding that PAE can regulate glucolipid metabolism and modulate the gut microbiota and metabolites in HFD-induced obese mice, and the results indicate that PAE can be used as a functional dietary supplement to alleviate HFD-induced obesity.