Obesity is a multifactorial chronic metabolic disease with multiple complications. Crataegus pinnatifida (CP) and Wolfiporia extensa (WE) are traditional functional foods with improving metabolic health properties. This study demonstrated the effect of CP and WE combination on ameliorating obesity induced by a high-fat diet (HFD). Moreover, the CP-WE food pair ameliorated HFD-induced metabolic disorders, including glucose intolerance, insulin resistance, hyperlipidemia, and hepatic steatosis. 16S rRNA gene amplicon sequencing and analysis revealed that CP combined with WE reshaped the composition of gut microbiota in HFD-fed mice. Furthermore, correlation analysis revealed a substantial association between the obesity-related parameters and the shifts in predominant bacterial genera influenced by the food pair intervention. In conclusion, this study demonstrated that the CP-WE food pair ameliorated HFD-induced obesity and reshaped gut microbiota composition, providing a promising approach to combat obesity through specific food combinations.