Shenhua compound, composed of ginseng, hawthorn and sophora flower, has been shown to improve hyperlipidemia. However, the main ingredients, their metabolic pathways in vivo, and pharmacokinetic characteristics. In this study, ultra-high-performance liquid chromatography coupled with electrospray ionization quadruple time-of-flight mass spectrometry (UHPLC-Q-TOF) was used to qualitatively analyze the main ingredients in ethanol extract of Shenhua compound and to investigate the metabolites in serum, bile, feces, and urine of rats following oral administration. The pharmacokinetics of ginsenoside Rg1, ginsenoside Re, ginsenoside Ro and rutin in rats were analyzed using triple-quadrupole liquid chromatography combined with electrospray ionization mass spectrometry (QQQ-LC/MS). The results indicated that 48 compounds were present in Shenhua compound, including saponins, flavonoids and organic acids. Metabolites were comprehensively analyzed after oral administration of Shenhua compound, and 24 prototype ingredients and 92 metabolite ingredients were identified or characterized. By analyzing the pharmacokinetic parameters of ginsenoside Rg1, ginsenoside Re, ginsenoside Ro and rutin from 0 to 72 h after oral administration of various dose of Shenhua compound, it was observed that the concentration of ginsenosides in blood remained below 2 ng∙mL1, but the metabolic excretion time was prolonged. Meanwhile, the blood concentration of rutin was significantly higher than ginsenosides and showed a double absorption peak. In conclusion, this study provides valuable insights into compound ingredients metabolism regularities in vivo and pharmacokinetics after oral administration of Shenhua compound.