Red clover consists of the overground parts and inflorescence of Trifolium pratense L., a leguminous plant belonging to the genus Trifolium. It is widely distributed worldwide and has long been used in traditional medicine. In this study, a combination approach using UPLC-MS and network pharmacology was applied to explore the quality control markers for the quality assessments of red clover. Firstly, UPLC-MS was used to identify the compounds in different parts of red clover. Twenty-eight compounds were totally identified. According to the traditional clinical efficacy of red clover, a compound-target-function network was constructed by network pharmacology to discover the main active compounds based on the identified compounds. Nine compounds of chlorogenic acid, daidzin, calycosin-7-O-β-d-glucoside, genistin, ononin, daidzein, genistein, formononetin, and biochanin A were filtrated and further confirmed in rat plasma in view of the blood-absorbed components taking effects. Finally, a novel method for simultaneously detecting the nine quality control markers was developed by UPLC-QQQ-MS in an effort to assess the quality of red clover. For all samples, the average contents of the nine compounds measured from high to low consist of formononetin, ononin, biochanin A, genistin, daidzin, calycosin-7-O-β-d-glucoside, genistein, daidzein, and chlorogenic acid. The samples from Gansu province showed the best quality in the three producing areas This study provides new strategies to explore the quality control markers and develops a novel method for the quality assessment of red clover.