Fuyuan Shenghua granule (FYSHG) is a clinical herbal formula adapted for medical abortion as an adjuvant treatment. This study aimed to screen the key active ingredients of FYSHG in treating medical abortion in vivo using ingredient-protein interaction and pharmacokinetics. The main ingredients of FYSHG absorbed in the blood were identified through UHPLC-Q-TOF/MS. An ingredient-target interaction network was constructed and analyzed to screen the key active ingredients of FYSHG in the treatment of medical abortion. The network was validated via molecular docking in silico and surface plasmon resonance (SPR) assays in vitro. Finally, the concentration was analyzed via UHPLC‒MS/MS, and pharmacokinetic characteristics including AUC, Cmax, MRT, T1/2 were calculated for further evaluation. In total, 34 active ingredients of FYSHG absorbed in the blood were identified via UHPLC-Q-TOF/MS. Among them, 6-gingerol (0.008 mg/g), 6-shogaol (0.012 mg/g), amygdalin (1.677 mg/g), astragaloside IV (0.022 mg/g), calycosin-7-glucoside (0.25 mg/g), and senkyunolide H (0.066 mg/g) were identified as the six key active ingredients of FYSHG. The Cmax values of these ingredients ranged from 42 to 288 µg/L, with t1/2 values ranging from 4.3 to 12.13 h, suggesting fast absorption, no obvious accumulation, and good drug-like properties. This study revealed that 6-gingerol, 6-shogaol, amygdalin, astragaloside IV, calycosin-7-glucoside, and senkyunolide H were six key active ingredients of FYSHG in vivo. These findings might contribute to the treatment of medical abortion.