Background The Synergy between Percutaneous Coronary Intervention (SYNTAX) score, has been used to estimate the extent and complexity of coronary artery disease (CAD). The H2FPEF score enables robust discrimination of heart failure with preserved ejection fraction (HFpEF) from non-cardiac aetiologies of dyspnea. In the present study, we aimed to investigate the relationship between H2FPEF and SYNTAX scores in patients with non-ST elevation myocardial infarction (NSTEMI). Method Two hundred eighty two consecutive patients with NSTEMI who underwent coronary angiographic examination were enrolled in this study. The H2FPEF score was calculated for each patient on admission. All patients underwent coronary angiography within 2 days following their admission. The SYNTAX scoring system was used to evaluate the severity and extent of CAD. Results The mean H2FPEF Score [3(2–4) vs 1(0.5–1.5), p < .001] and the frequencies of diabetes mellitus, hypertension and, atrial fibrillation were significantly higher and LVEF was significantly lower in patients with high SYNTAX score. High H2FPEF Score (OR: 3.61, 95%CI: 2.64–4.93; p = .001) and low left ventricular ejection fraction (OR: 0.94, 95%CI: 0.89–0.98; p = .013) were found to be independent associates for high SYNTAX score. H2FPEF Score above a cut-off level of 2.5 predicted high SYNTAX score with a sensitivity of 80% and a specificity of 82.5% (AUC: 0.890; 95%CI: 0.848–0.931; p < .001). There was a significant and moderate positive correlation between H2FPEF and SYNTAX Scores (r = 0.694, p < .001). Conclusion High H2FPEF score may be associated with high SYNTAX score and may be used to estimate the extent and complexity of CAD in NSTEMI patients.