Wine/zingiberis rhizoma recens/euodiae fructus processed Coptidis Rhizoma (wCR/zCR/eCR) are the major processed products of CR in clinic, and the role of CR is highlighted in different aspects after being processed with different excipients. To explore the mechanism and material basis for the highlighted efficacy of wCR/zCR/eCR, the metabolomics strategy was introduced to the comparative study between wCR/zCR/eCR and CR. Firstly, the metabolomics approach was applied to compare the chemical profiling and differential components between wCR/zCR/eCR and CR extract. Secondly, the rats were treated with CR/wCR/zCR/eCR extracts and a serum metabolomics approach was adopted to compare the metabolic profiling and significantly changed metabolites in CR/wCR/zCR/eCR groups, base on which the metabolic pathways were enriched, the metabolic network was constructed and the highlighted efficacy wCR/zCR/eCR was investigated. Lastly, the pathological and biochemical assessments (VIP, COX, HSL and HMGR) were implemented to validate the results inferred from metabolomics study. In chemical research, 23 differential components between wCR/zCR/eCR and CR extracts were identified. Thereinto, the content of alkaloids and organic acids decreased in wCR extract, the content of partial alkaloids and most organic acids increased in zCR extract, the content of alkaloids decreased, and partial organic acids increased in eCR extract. In serum metabolomics study, wCR had no outstanding effect, zCR played a more prominent role in resisting inflammation of gastrointestinal tissue by interfering with arachidonic acid metabolism, eCR exhibited the hottest drug property and the strongest effect on smoothing the liver and harmonizing the stomach by interfering with of bile acids biosynthesis. Based on the changes in chemical composition and efficacy before and after processing, as well as biochemical validation, it can be concluded that the above activity of zCR might be related to the increased alkaloids and organic acids in zCR extract, and the prominent role of eCR may be related to the increased organic acids in eCR extract. In brief, hot processing excipients could alleviate the cold property of CR, and different excipients have different effects on the chemical composition and efficacy mechanism. The present study fully reflects the advantage of metabolomics and provides guidance for the rational use of CR.