Aim To analyze and to compare the application of fractional flow reserve （FFR） and coronary angiography （CAG） on instructing the treatment of borderline lesion of left main coronary artery. Methods 187 patients with borderline lesions in left main coronary artery confirmed by the CAG were divided into four groups: CAG medicine treatment group,CAG intervention group,FFR medicine treatment group,FFR intervention group. CAG medicine treatment group was treated merely with optimal secondary prevention medicine for coronary artery disease,but no percutaneous coronary intervention （PCI）. CAG intervention group accepted PCI according to the operator's experience,the patient's clinical symptoms and the related auxiliary examination. FFR medicine treatment group was treated with medicine therapy according to FFR value＞0.80. FFR intervention group was treated with PCI according to FFR value≤0.80. All patients were given optimal secondary prevention medicine for coronary heart disease. Main adverse cardiac event （including cardiovascular death,non-fatal myocardial infarction,target vessel revascularization） and angina pectoris classification of Canadian Cardiovascular Society （CCS） were analyzed in the 12 months follow-up period. Results The 4 groups had no cardiovascular death and CCS Ⅳ grade angina pectoris attack. Compared with CAG-guided medicine treatment group and intervention group,non-fatal myocardial infarction,target vessel revascularization and CCS Ⅰ～Ⅲ grade angina pectoris decreased significantly in FFR-guided medicine treatment group and intervention group （P<0.05）. Conclusion FFR have a certain guiding significanc in the therapy of borderline lesion of left main coronary artery.