Aim To investigate the shared transcriptional characteristics of non-alcoholic fatty liver disease (NAFLD) and atherosclerosis (As) using bioinformatics techniques. The goal is to identify potential mechanisms and key targets of As that are linked to NAFLD through gene crosstalk analysis of both diseases. Additionally, the study will validate the expression levels of these key targets in animal tissues and human serum samples. Methods The gene expression profiles of NAFLD (dataset GSE89632) and As (dataset GSE43292) were obtained from GEO database. Differential gene analysis and weighted gene co-expression network analysis were conducted to identify common genes between the two diseases. These shared genes were further analyzed using the String database for protein interaction analysis and R software. Core genes were identified through calculations in Cytoscape software, validation with external datasets (GSE100927), and machine learning techniques (LASSO regression). Finally, key core genes were determined by creating nonalcoholic fatty liver and As mouse models on a high-fat diet and collecting peripheral serum samples from patients with NAFLD and coronary heart disease (CHD). Results Seventy-five shared genes were identified between the two diseases, with major enrichment pathways including cytokine-cytokine receptor interaction, IL-17 signaling pathway, lipid and atherosclerosis, and NF-κB signaling pathway. Through integration of multiple bioinformatics methods, two core genes (MMP-9 and CCL3) were identified. Subsequent animal experiments demonstrated a significant increase in MMP-9 and CCL3 levels in the liver and aortic sinus of mice fed with high-fat diet, MMP-9 and CCL3 levels in the liver tissue of high-fat diet-fed mice were 2.43 times (P＜0.001) and 1.35 times (P＜0.01) higher than the control group, in the aortic sinus tissue, MMP-9 and CCL3 levels were 2.10 times (P＜0.001) and 1.58 times (P＜0.01) higher. Human serum sample verification further supported these findings, showing MMP-9 and CCL3 levels in patients with both NAFLD and CHD to be 1.21 times (P＜0.01) and 1.29 times (P＜0.01) higher than in patients with CHD alone. Conclusion This study identified MMP-9 and CCL3 may play key roles in NAFLD-related As, providing potential targets for the study of NAFLD-related As.