Objective To explore the association between the expression levels of serum S100 calcium-binding protein A12(S100A12), 20-hydroxyeicosatetraenoic acid (20-HETE), and microRNA-647 (miR-647) and postoperative instent restenosis (ISR) in patients undergoing coronary drug-eluting stent (DES) implantation, with a focus on excluding the confounding effects of hypertension, diabetes mellitus, and related medications. Methods A total of 116 patients with coronary heart disease (CHD) scheduled for DES implantation (CHD group) and 116 healthy individuals who underwent physical examination during the same period (control group) were selected from March 2023 to March 2024. The levels of serum S100A12, 20-HETE, miR-647, high-sensitivity C-reactive protein (hs-CRP), and interleukin-6 (IL-6) in fasting venous blood were detected (once on the day before surgery and once on the first day after surgery in the CHD group, and once in the control group). The CHD group was followed up for 1 year and divided into the ISR group (16 cases) and non-ISR group (100 cases) according to the occurrence of ISR. Stratified multivariate Logistic regression was used to exclude confounding factors, subgroup analysis was conducted to verify the stability of conclusions, and ROC curves were used to evaluate the predictive value of the indicators. Results The levels of S100A12, 20-HETE, and miR-647 in the CHD group were significantly higher than those in the control group before surgery, but these indicators decreased significantly after surgery compared to pre-surgery levels. . The incidence of ISR was 13.79%, and there were no significant differences in the course of hypertension/diabetes mellitus or medication type between the ISR group and non-ISR group. The fully adjusted multivariate model showed that postoperative S100A12(OR=1.468, 95%CI: 1.054-2.045), 20-HETE (OR=1.461, 95%CI: 1.015-2.103), and miR-647 (OR=1.425, 95%CI: 1.049-1.934) were independent risk factors for ISR (all P<0.05). Subgroup analysis showed that the association between the core indicators and ISR was stable in populations with or without hypertension/diabetes mellitus (all P interaction>0.05). ROC curve analysis showed that the AUC of postoperative S100A12 for predicting ISR was 0.896 (sensitivity: 83.33%, specificity: 83.72%). Conclusion After excluding the confounding effects of hypertension, diabetes mellitus, and related medications, serum S100A12, 20-HETE, and miR-647 remain independent influencing factors for ISR in CHD patients after DES implantation. Among them, S100A12 has the optimal predictive efficiency and can be used as a preferred biomarker for clinical ISR risk stratification.