Objective To evaluate the predictive value of SYNTAX score (SXscore) and clinical SYNTAX score (CCS) in the primary endpoint events of coronary heart disease patients in 15 months after percutaneous coronary intervention (PCI). Methods A total of 547 patients undergoing selective or emergency PCI in our department from June 2009 to June 2011 were enrolled in this study. SXscore and CCS were carried out to grade the severity and extension of stenosis. The major adverse cardiac and cerebrovascular events (MACCE, including cardiac death, myocardial infarction, and revascularization and stroke from any cause), the secondary endpoint events (including target lesion failure, such as cardiac death and target-vessel driven myocardial infarction, and ischemia-driven target lesion revascularization), stent thrombosis, and hospitalization due to angina pectoris were observed during 15 months of follow-up by telephone or hospital visit. Results In the follow-up, the incidence of MACCE was 13.5%, 6.8% and 0.0%, respectively for those with high, medium and low scores in SXscore (P＜0.0001). After multivariable adjustment, the SXscore (RR=1.101, 95%CI 1.070～1.134; P＜0.0001) and CSS (RR=1.017, 95%CI 1.009～1.022; P＜0.0001) were both identified as independent predictor of MACCE. Conclusion Both SXscore and CSS are independent predictor of MACCE for coronary heart disease patients after PCI.