Objective To observe a series of correlated index and to evaluate the effects of two heparin doses during cardiopulmonary bypass (CPB) surgery. Methods Sixty patients eligible for CPB surgery were divided randomly into low-dose heparin (2 mg/kg, n=30) group and conventional heparin (3 mg/kg, n=30) group. The function of blood coagulation during and after surgery, activated coagulation time (ACT) after injection of haparin, the total heparin doses, the protamine doses, the microembolus filter screen adhesion degrees, transfusion of allogeneic blood, platelet counts (PLT), the amount of postoperative chest drainage at 24 h, mortality and morbidity were recorded for the two groups. Results In the low-dose heparin group, only one patient was unsufficient to achieve target ACT while target ACT was achieved in all the patients of the conventional group. No complication of myocardial infarction, cerebral and pulmonary embolism was detected in the patients during the operation and postoperation. There was no difference between the two groups in terms of the microembolus screen pack cleaning degree, postoperative blood transfusion, postoperative chest drainage at 24h and platelet counts (PLT), yet the ACT values after heparin administration of the low-dose heparin group was lower than the conventional group. The total heparin dose and the blood transfusion intraoperation were remarkably reduced in the low-dose group. The differences of prothrombin time (PT) at CPB20min and postoperative 24h, fibrinogen (Fib) at CPB 40 min and postoperative 24h in the two groups were significant. Conclusions Compared with conventional heparin (3mg/kg), most patients in low dose heparin (2mg/kg) can reach target ACT (400s) after injection of initial heparin, meet the demand of CPB surgery, and also reduce blood coagulation disorders and blood transfusion intraoperation.