This study explored the quality markers of Lepidii Semen in the treatment of heart failure using UPLC-Q-TOF-MS/MS and network pharmacology approaches. A rat model of heart failure was established via intraperitoneal injection of monocrotaline. Right cardiac function was assessed using small-animal ultrasound imaging. Pathological injuries in the heart and lungs were evaluated via hematoxylin-eosin staining. Serum levels of brain natriuretic peptide (BNP) and N-terminal pro-BNP (NT-proBNP) were measured using ELISA. UPLC-Q-TOF-MS/MS was employed to identify blood-absorbed ingredient in serum samples from the normal control and water extract of Lepidii Semen (LSWE). A component-target-pathway network was constructed using network pharmacology, and molecular docking was performed to validate interactions between core components and key targets. Compared with the model group, the LSWE group exhibited significantly reduced mean pulmonary arterial pressure and right ventricular hypertrophy index, along with increased ratios of pulmonary artery acceleration time to ejection time, right ventricular internal diameter to left ventricular internal diameter, and right ventricular outflow tract cardiac output. Serum BNP and NT-proBNP levels were also significantly decreased. Twenty-six blood-absorbed components were identified in the LSWE group, including flavonoids, uridine derivatives, lignans, alkaloids, glucosinolates, and cardenolides. Network pharmacology revealed that eight active components, such as cis-desulfoglucotropaeolin, lepidiumbenzamide E, and quercetin-3-O-[2-O-(6-O-E-sinapoyl)-β-D-glucopyranosyl]-β-D-glucoside, might exert anti-heart failure effects by targeting protein kinase B1 (AKT1), epidermal growth factor receptor (EGFR), and estrogen receptor 1 (ESR1), matrix metalloproteinase 9 (MMP9), MMP2, modulating signaling pathways including diabetic cardiomyopathy, advanced glycosylation end products/receptor of AGEs (AGE-RAGE), and TNF (tumor necrosis factor). Molecular docking demonstrated the lowest binding energies for cis-desulfoglucotropaeolin with AKT1, lepidiumbenzamide E with ESR1/MMP2/MMP9/PPARG, and quercetin-3-O-[2-O-(6-O-E-sinapoyl)-β-D-glucopyranosyl]-β-D-glucoside with EGFR/TNF. The active components of Lepidii Semen likely combat heart failure by targeting AKT1 and regulating inflammation-, immunity-, and cancer-related pathways. cis-Desulfoglucotropaeolin, lepidiumbenzamide E, and quercetin-3-O-[2-O-(6-O-E-sinapoyl)-β-D-glucopyranosyl]-β-D-glucoside may serve as potential quality markers for further investigation into the anti-heart failure properties of Lepidii Semen.