Herbal pairs are combinations of two relatively fixed herbs that are frequently used in clinical practice to achieve specific therapeutic effect. Epimedium and Astragalus are frequently used together in clinical settings. However, there is a lack of an in-depth understanding of the active components of these herbs in vivo. In this study, a method based on ultra-high-performance liquid chromatography coupled to high resolution mass spectrometry together with diagnostic fragment ions (DFIs) mass defect filtering (MDF) was developed to systematically screen and identify the chemical ingredients presenting in Epimedium-Astragalus granule pair (EAGP) and the absorbed components and their metabolites in rat plasma following oral administration. Using accurate mass determination, mass defect filtering and diagnostic fragment ion screening strategies, a total of eighty-five ingredients were identified in EAGP. By comparing the total ion chromatograms obtained from dosed rat plasma, blank rat plasma and EAGP solution, a total of forty-six compounds were detected in dosed rat plasma, including twenty-five prototypes and twenty-one metabolites. Among these, seventeen parent compounds were derived from Epimedium and eight were from Astragalus. These metabolites were associated with ononin (M1, M2, M9 M10 and M17), calycosin-7-O-β-D-glucoside (M6, M7, M8 and M13), icariin (M3, M4, M5, M11, M14, M15, M18, M19, M20 and M21) and methylnissolin (M12). The metabolic pathways included hydroxylation, demethylation, deglycosylation and glucuronidation. This study elucidated the potential pharmacologically active components of EAGP and provided essential data for the further study on its pharmacological materials basis and mechanism of action.