Primary dysmenorrhea (PD) has a prevalence of up to 90％ in the adolescents.Chinese herbal formula, namely Shaofu Zhuyu formula, is an effective prescriptionfor treating PD patients. Here, the metabolomics tool was used to explorepathogenesis of PD and the clinical efficacy of SFZYFG. The study was conductedJiangsu Provincial Hospital of Integrated Traditional and Western Medicine, andwhich was complied with guidelines of Good Clinical Practice. Twenty-fourpatients, mean age 23.8 ± 3.03 (SD) and twelve healthy volunteers (aged 24.3 ± 2.12)participated in the study. Blood and urine samples were collected from each subjecton the first day of menstrual cycle for continuous 4 periods. The metabolic profilingdata stated that endogenous metabolites have changed in PD patients. The totalbiomarkers (19 in plasma and 16 in urine) , up regulated or down regulated (p < 0.05or 0.01), were identified and contributed to PD progress. These promising biomarkercandidates are closely related to sphingolipid metabolism, seroid hormonebiosynthesis, and glycerophospholipid metabolism. In addition, twenty-four alteredmetabolites were restored back to the healthy level, and fourteen clinical biochemicalindicators were regulated significantly after the treatment of SFZYFG. Altogether,results not only gave rise to a systematic view of the development of PD diseasealso provided the theoretical basis to improve the whole status in these patients.