Untargeted metabolomics analysis of rhubarb and stewed rhubarb samples shows that the determined samples clearly clustered in to two groups, indicating that the processing procedures caused changes in the composition and/or content of components in rhubarb. Ten components were identified by UHPLC-Q-TOF-MS/MS and references, which intensity declined in rhubarb after processing. Targeted metabolomics analysis of rhubarb and stewed rhubarb samples indicated that aloe-emodin, rhein, emodin and physcion were detected with lower intensity in stewed rhubarb samples than in rhubarb samples. Metabolomics analysis of rhubarb and stewed rhubarb indicated the various components of rhubarb changed after processing.