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In this study, RNA-seq technology was used to study the protective effect of Compound Longmaining (CLMN) decoction on acute myocardial infarction (AMI). The results of RNA-seq showed that the CLMN decoction has a regulatory effect on the 51 differentially expressed genes (DEGs), which were mainly enriched in the 7 pathways revealed by KEGG analysis. In addition, qPCR technology was used to verify the expression of chemokine (C-C motif) ligand 6 (Ccl6), chemokine (C-C motif) receptor 5 (Ccr5), integrin alpha M (Itgam), neutrophil cytosolic factor 1 (Ncf1), and matrix metallopeptidase 9 (Mmp9). Experiment data showed that the qPCR results were consistent with the RNA-seq results. This study demonstrated that CLMN decoction might regulate the expressions of Ccl6, Ccr5, Itgam, Ncf1 and Mmp9, inhibit the chemokine signaling pathway and leukocyte transendothelial migration to play a protective effect on AMI.