Aim To investigate the changes of serum miR-1, miR-133a and miR-208a levels in patients undergoing on-pump coronary artery bypass surgery (ONCABG) and off-pump coronary artery bypass grafting (OPCABG). Methods From February 2016 to February 9,4 patients with multiple coronary artery disease requiring CABG in our hospital were selected. According to the operation method, 94 patients were divided into ONCABG group (n＝47) and OPCABG group (n＝47). The serum miR-1, miR-133a and miR-208a levels were detected by quantitative real-time PCR in all patients before operation and at different time after operation. The levels of serum cardiac troponin I (cTnI) and creatine kinase isoenzyme MB (CK-MB) were detected by chemiluminescence immunoassay in all patients before operation and at different time after operation. The correlation between serum miR-1, miR-133a, miR-208a levels and cTnI, CK-MB levels was analyzed. Results Compared with preoperative, the serum levels of miR-1, miR-133a, miR-208a, cTnI and CK-MB were increased in both groups at 4 h and 24 h after operation (P＜0.05). Compared with 4 h after operation, the serum levels of miR-1, miR-133a, miR-208a, cTnI, and CK-MB were decreased in the two groups at 24 h after operation (P＜0.05). Compared with ONCABG group, the serum levels of miR-1, miR-133a, miR-208a, cTnI and CK-MB were lower in OPCABG group at 4 h and 24 h after operation (P＜0.05). Pearson analysis showed that the serum miR-1, miR-133a and miR-208a levels were positively correlated with cTnI and CK-MB levels at 4 h and 24 h after operation in the two groups (P＜0.05). Conclusion miR-1, miR-133a, and miR-208a are expected to be important biomarkers for judging myocardial injury after ONCABG and OPCABG. This study provides a certain reference for the clinical selection of ONCABG and OPCABG.