Cardiac glycosides from Periplocae Cortex are bioactive constituents, but isolating and structurally confirming their trace in vivo metabolites remains challenging because authentic standards are often unavailable. We developed a steroid-core fragment-guided strategy based on the diagnostic ion at m/z 355.2270 that integrates metabolite screening, targeted purification, and structural characterization. Periplocin-related analytes were detected in rat urine and plasma after oral periplocin administration using HPLC-QQQ-MS/MS and UPLC-Q-TOF-MS/MS. Guided by the diagnostic ion, 13 L of rat urine was fractionated using macroporous resin, Sephadex LH-20, ODS chromatography, and preparative HPLC. Two trace metabolites were isolated and identified as gomphogenin (M1, 4 mg) and 17α-asclepioside (M2, 8 mg) by HR-MS and NMR spectroscopy. Periplocin, periplogenin, and periplocymarin were confirmed using reference standards. Structural comparison supported a putative transformation pathway involving deglycosylation and steroid-core modification. In a hypoxia/reoxygenation-injured H9c2 cell model, M1 and M2 increased cell viability at 50 μM, supporting further evaluation using complementary cellular endpoints. This diagnostic-ion-guided workflow enables the targeted isolation of trace cardenolide metabolites from biological matrices and provides reference compounds for future pharmacokinetic and pharmacological studies.