Objective To investigate the mechanism of Traditional Chinese Medicine in improving lipid metabolism in atherosclerosis (AS) based on data mining, network pharmacology, molecular docking, and animal experiments. Methods Data mining was used to screen literature on Traditional Chinese Medicine intervention in AS lipid metabolism. Statistical analysis was performed on the use frequency of prescription drugs, as well as properties, flavors, and meridian entries of high⁃frequency drugs. The Apriori algorithm was applied to analyze association rules among high⁃frequency drugs and identify the most frequently used drug combination. The chemical components and effect targets of the most high⁃frequency used drug combination were collected using the TCMSP and BATMAN⁃TCM databases. Targets related to AS lipid metabolism were retrieved from the GeneCards® and OMIM® databases. Intersection between drug effect targets and disease⁃related targets were obtained using R language software to identify core targets. The data of the active components and core targets were imported into Cytoscape software to construct a “Traditional Chinese Medicine active component⁃core target” network. A protein⁃protein interaction (PPI) network of core targets was constructed using the STRING database. Enrichment analysis of core targets was performed using R language software and Perl programs, and molecular docking was conducted using AutoDock software. A total of 27 mice were randomly divided into three groups: blank group, model group, and Pinellia ternata⁃Citrus reticulata group, with 9 mice in each group. The blank group was fed a normal diet, while the model group and Pinellia ternata⁃Citrus reticulata group were fed a high⁃fat diet for 16 weeks. At week 8 of feeding, the Pinellia ternata⁃Citrus reticulata group received intragastric administration of 200 μL/d Pinellia ternata⁃Citrus reticulata decoction, while the blank group and model group received an equal volume of sterile 0.9% sodium chloride solution for 8 consecutive weeks. Two hours after the last administration, blood lipid levels in mice were measured. The conditions of aortic plaque in the heart tissue was observed using oil red O staining and HE staining. Western blot was performed to detect the relative protein expressions of peroxisome proliferator⁃activated receptor γ (PPARγ), liver X receptor α (LXRα), and ATP⁃binding cassette transporter A1 (ABCA1) in the aorta tissues of mice. Results A total of 125 Traditional Chinese Medicine clinical prescriptions were retrieved. The properties of the prescription drugs were mainly warm and cold, while the flavors were primarily bitter, sweet, and acrid. These drugs were mainly attributed to the liver, spleen, and heart meridians. The Pinellia ternata⁃Citrus reticulata drug pair was the most frequently used drug combination. A total of 96 core targets of Pinellia ternata⁃Citrus reticulata in improving AS lipid metabolism were identified. The top five active components in the “Traditional Chinese Medicine active component⁃core target” network topology analysis were stigmasterol, baicalein, cycloartenol, cis⁃11⁃eicosenoic acid, and nobiletin. The top 10 targets ranked by degree values in the PPI network topology analysis included AKT1, TP53, PPARγ, CASP3, VEGFA, ESR1, FOS, MAPK3, HIF1α, and CREB1. Enrichment analysis results revealed that core targets were mainly involved in biological processes such as responses to different nutrient levels, steroid hormones, and metal ions; cellular structures such as membrane rafts, membrane microdomains, and synaptic membranes; in addition, molecular functions such as DNA⁃binding transcription factor binding, nuclear receptor activity, and ligand⁃activated transcription factor activity. Enriched signaling pathways included lipid and atherosclerosis, phosphatidylinositol 3⁃kinase/protein kinase B signaling pathway, etc. Molecular docking results indicated that baicalein, the core active component of Pinellia ternata⁃Citrus reticulata, exhibited the most stable binding with PPARγ. Animal experiment results expressed that compared with the model group, the Pinellia ternata⁃Citrus reticulata group and blank group exhibited decreased levels of TG, TC, and LDL⁃C, elevated HDL⁃C level, decreased relative area of aortic atherosclerotic plaques, and elevated relative protein expressions of PPARγ, LXRα, and ABCA1 in the aorta tissues (P<0.05). Conclusion The Pinellia ternata⁃Citrus reticulata drug pair effectively ameliorates lipid metabolism in AS by regulating the PPARγ⁃LXRα⁃ABCA1 signaling pathway.