Abstract: Huatan Jiangzhuo decoction (HJD) is a combination of six traditional Chinese medicines that were used for lipid metabolism-related disorders, but its efficacy and underlying mechanisms have not been explored by modern research strategies. This study aimed to investigate the therapeutic role of HJD in determining the transcriptome level. Hyperlipidemia model was established by feeding Sprague–Dawley rats with high-fat diet. Differentially expressed genes (DEGs) were detected by high-through transcriptome sequencing, followed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The total cholesterol (TC) and triglyceride (TG) levels in hyperlipidemia model rats were significantly increased, whereas high-density lipoprotein (HDL) concentration decreased when compared to normal rats, and HJD significantly downregulated TC concentrations and liver coefficient in the hyperlipidemia rats. Histology staining showed that HDJ greatly recovered the lipid accumulation in rat hepatic stellate cells and aortic arch vascular wall thickness of hyperlipidemia rats. One thousand nine hundred and thirty-six DEGs were identified in the HJD-treated hyperlipidemia rats, which were associated with various biological processes and signaling pathways such as peroxisome proliferator-activated receptors, AMP-activated Protein Kinase , and insulin signaling pathways. Quantitative reverse transcription–polymerase chain reaction further confirmed the downregulated expression of cholesterol 7-α-hydroxylase (CYP7A1), liver orphan receptor (LXRα), peroxisome proliferator-activated receptor gamma (PPARγ), and Sterol Response Element-Binding Protein 1c (SREBP1c) genes in hyperlipidemia rats treated with HJD. Our data first elucidated the gene expression profile of high-fat diet-induced hyperlipidemia in rats after HJD treatment, and lipid metabolism-related genes (CYP7A1, LXRα, PPARγ, and SREBP1c) may be potentially biomarkers for HJD-alleviated hyperlipidemia.