In recent years, the increasing obese and overweight population has become a worldwide public health problem, as there is no effective medication to control obesity. Auricularia heimuer is rich in active substances that have potential biologically active functions. The anti-obesity effect and mechanism of Auricularia heimuer fruiting body alcohol extraction (AHA, 150–600 mg/kg·bw) was investigated in obese mice by assessing changes in endogenous liver metabolites using a liquid chromatography-tandem mass spectrometry approach. The aim of this study was to identify an effective food to control human obesity. AHA of 600 mg/kg·bw (HC) significantly decreased body weight and improved serum biochemistry indices. Sixty-eight liver metabolites were identified and significantly separated among the normal, high-fat diet (HFD), and HC groups. Moreover, the metabolic analysis revealed that HC significantly regulated specific metabolites in mice including amino acids, lipids, and carbohydrate compounds. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that HC was significantly involved in different metabolite pathways including arachidonic acid metabolism, galactose metabolism, carbohydrate digestion and absorption, linoleic acid metabolism, and starch and sucrose metabolism. Eight weeks after supplementing with HC, major metabolites in related pathways that were disrupted by an HFD were restored to normal levels, suggesting that HC had anti-obesity activity.