The enhanced efficacy of vinegar‐processed Cyperus rotundus (VCR) in treating primary dysmenorrhea (PD) has been observed. However, the active components and potential mechanisms of synergy are still unclear. The objective of this study was to develop a method that combines bionic technology, plant metabolomics and network pharmacology to discover the active components and potential mechanisms underlying the enhanced therapeutic effects of VCR for PD. Vinegar processing alters the flavor of C. rotundus, leading to changes in its properties. The acidic nature of vinegar enhances the selectivity of the medicine toward the liver, thereby improving its ability to soothe the liver, regulate qi and provide pain relief. Through gas chromatography–mass spectrometry and multivariate statistical analysis, 30 key differential components between raw C. rotundus and VCR have been screened and identified. These differential components primarily exert their therapeutic effects in treating PD by modulating targets such as interleukin‐6, TNF, TP53 and PTGS2, as well as pathways including the estrogen signaling pathway, ovarian steroidogenesis, the TNF signaling pathway and the HIF‐1 signaling pathway. The findings of this study serve as a reference for the application of VCR in compound formulas and clinic practiceal. Furthermore, the methodology employed in this study provides research insights for the processing of other Chinese medicines.