Objective To investigate the effects of the transplantation of autologous and allogeneic adipose-derived mesenchymal stem cells (ADMSCs) on the cardiac function in rats with acute myocardial infarction (AMI). Methods Firstly, ADMSCs were isolated from BN and Lewis rats, and the third generation were labeled with CM-DiI. Then 45 male Lewis rats were randomly divided into 3 groups (control group, autologous cell transplantation group, and allogeneic cell transplantation group). The AMI model was established by ligating the rats' left anterior descending artery, and then the infarcted myocardium as well as the peripheral parts was injected by the labeled ADMSCs via the endocardium. At 7 days after ADMSC transplantation, the infiltration of CD4+ T lymphocytes, CD8+ T lymphocytes and CD68+ macrophages were detected by immunofluorescence technique. At 7, 14 and 28 days after transplantation, survival rate of the transplanted cells was compared. Then echocardiography was used to detect the rats' cardiac function at 28 days after transplantation. And the expression of α-smooth muscle actin (α-SMA) was detected by immunofluorescence technique for determining the angiogenesis near the transplanted cells. Results The positive rate of the cells labeled with CM-DiI was nearly 100%. At 7 days after transplantation, lymphocyte infiltration and macrophages were observed around the transplanted cells in the allogeneic cell transplantation group. No lymphocyte infiltration and macrophages were observed in the autologous cell transplantation group. Compared with allogeneic cell transplantation, the survival rate of the transplanted cells increased significantly. Moreover, the left ventricular short axis shortening rate (LVFS) and the diastolic left ventricular anterior wall thickness (LVAWTd) increased at 7, 14 and 28 days after transplantation. Meanwhile, the number of angiogenesis around the infarcted myocardium also significantly increased. Conclusion Autologous ADMSC transplantation is significantly better at improving cardiac function in AMI rats than allogeneic ADMSC transplantation.