Intra-operative autologous blood donation is a blood conservation technique with limited evidence. We evaluated the association between intra-operative autologous blood donation and decrease in peri-operative transfusion in cardiovascular surgery based on evidence from a Japanese administrative database. We extracted the data of patients who had undergone cardiovascular surgery from the Diagnosis Procedure Combination database in Japan (2016–2019). Based on the surgery type, we examined the association of intra-operative autologous blood donation with the transfusion rate and amount of blood used in cardiac and aortic surgeries using multilevel propensity score matching. We enrolled 32,433 and 4,267 patients who underwent cardiac and aortic surgeries and received 5.0% and 6.7% intra-operative autologous blood donation with mean volumes of 557.68 mL and 616.96 mL, respectively. The red blood cell transfusion rates of the control and intra-operative autologous blood donation groups were 60.6% and 38.4%, respectively, in the cardiac surgery cohort (p < .001) and 91.4%, and 83.8%, respectively, in the aortic surgery cohort (p = .037). The transfusion amounts for the control and intra-operative autologous blood donation groups were 5.9 and 3.5 units of red blood cells, respectively, for cardiac surgery patients (p < .001) and 11.9 and 7.9 units, respectively, for aortic surgery patients (p < .001). Intra-operative autologous blood donation could reduce the transfusion rate or amount of red blood cells and fresh frozen plasma for patients undergoing index cardiovascular surgery and could be an effective blood transfusion strategy in cardiovascular surgery for Japanese patients.