Objective To investigate the differentially expressed genes (DEGs) and their molecular interactions in unstable carotid atherosclerotic plaques. Methods Gene expression datasets related to carotid atherosclerotic plaques (GSE41571, GSE118481, and E-MTAB-2055) were downloaded from Gene Expression Omnibus (GEO) and European Bioinformatics Institute (EBI) ArrayExpress databases. The co-regulated DEGs in at least two datasets of unstable carotid plaques were merged and analyzed using Gene Ontology Biological Process (GO-BP), Kyoto Encyclopedia of Genes and Genomes (KEGG), Protein-Protein Interaction (PPI) Networks and subnetwork analysis, relationships between miRNAs/transcription factors and target genes, and drug-gene interaction database. Quantitative real-time PCR (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA) were used to detect the expression levels of some DEGs in carotid plaques and plasma from 58 patients with carotid atherosclerosis. Results GO enrichment analysis showed that DEGs in unstable carotid atherosclerotic plaques were mainly enriched in genes related to inflammatory response and extracellular matrix structure genes. KEGG enrichment analysis indicated that upregulated DEGs in unstable carotid plaques were enriched in extracellular matrix receptor (ECM-receptor) interaction, PI3K-Akt, Hippo and transforming growth factor-β (TGF-β) signaling pathways, while downregulated DEGs were primarily enriched in lysosomes, phagosomes, and chemokines processes. PPI network analysis suggested that COL1A2, COL4A2, insulin-like growth factor binding protein 6 (IGFBP6), COL4A5, C1QA, CXCL10, CXCL2, CXCR4, and CSF1R may play important roles in PPI networks. Prediction of drug-gene interactions revealed that CSF1R had the most drug interaction, CXCL2 was most antagonized by drugs, and IGFBP6 was most activated by drugs. qRT-PCR showed that the expression level of IGFBP6 in unstable carotid plaques group was significantly lower than that in stable carotid plaques group (P<0.001). ELISA results showed that plasma concentration of IGFBP6 in unstable carotid plaques group was significantly lower than that in stable carotid plaques group (P<0.0001). Receiver operating characteristic (ROC) suggested that the area under the curve (AUC) for plasma IGFBP6 levels to identify unstable plaques was 0.894 (95%CI 0.810-0.977), with a cutoff value of 142.08 ng/ml. Conclusion IGFBP6 may become an important biomarker for predicting unstable carotid atherosclerotic plaques.