Objective To investigate the secondary prevention and risk factor control in the patients with coronary artery diseases in order to analyze the differences between real world practice and evidence-based guidelines. Methods The patients with coronary angiography-diagnosed coronary heart disease hospitalized in our department during May 2010 to February 2011 were enrolled in this study. Their smoking condition, blood pressure, blood glucose, blood lipids and other risk factors during hospitalization and follow-up, and their medical treatment within 6 months after discharge were studied and analyzed. Results There were totally 128 patients being followed up. At discharge, the percentage of using aspirin, clopidogrel, beta blocker, ACEI/ARB and statins in their prescription was 91.41%, 97.66%, 67.19%, 65.63% and 97.66% respectively, and at the follow-up, the percentage changed to 87.50%, 83.59%, 57.03%, 57.81% and 85.16% respectively. The rate of smoking was decreased from 31.25% in hospitalization to 6.25% at follow-up, while the rate of normal blood pressure was increased from 54.69% in hospitalization to 75.78% at follow-up. The rate of the patients complicated with diabetes mellitus was 17.19% at discharge, and then increased to 27.27% at follow-up. During follow-up, there were 78.91%, 69.53% and 70.31% of the total patients who had normal levels of TC, TG and LDL-C. Conclusion Most patients comply to the medical treatment of secondary prevention during follow-up. And most risk factors are under well control. Prompt and effective measures should be taken to enhance medical education for secondary prevention to minimize the gap between clinical practice and evidence-based guidelines.