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PCSK9 is a promising target for developing novel cholesterol-lowering drugs. We developed a recipe that combined molecular docking, GC-MS/MS, and real-time PCR to identify potential PCSK9 inhibitors for herb ratio determination. Three herbs, <i>Carthamus tinctorius</i>, <i>Coscinium fenestratum</i>, and <i>Zingiber officinale,</i> were used in this study. This work aimed to evaluate cholesterol-lowering through a PCSK9 inhibitory mechanism of these three herbs for defining a suitable ratio. Chemical constituents were identified using GC-MS/MS. The PCSK9 inhibitory potential of the compounds was determined using molecular docking, real-time PCR, and Oil red O staining. It has been shown that most of the active compounds of <i>C. fenestratum</i> and <i>Z. officinale</i> inhibit PCSK9 when extracted with water, and <i>C. fenestratum</i> has been shown to yield tetraacetyl-d-xylonic nitrile (27.92%) and inositol, 1-deoxy-(24.89%). These compounds could inhibit PCSK9 through the binding of 6 and 5 hydrogen bonds, respectively, while the active compound in <i>Z. officinale</i> is 2-Formyl-9-[.beta.-d-ribofuranosyl] hypoxanthine (4.37%) inhibits PCSK9 by forming 8 hydrogen bonds. These results suggest that a recipe comprising three parts <i>C. fenestratum</i>, two parts <i>Z. officinale</i>, and one part <i>C. tinctorius</i> is a suitable herbal ratio for reducing lipid levels in the bloodstream through a PCSK9 inhibitory mechanism.