Low heart rate is a risk factor of mortality in many cardiovascular diseases. However, the relationship of minimum heart rate (MHR) with outcomes after cardiac surgery is still unclear, and the association between optimum MHR and risk of mortality in patients receiving cardiac surgery remains unknown. In this retrospective study using the Multi-parameter Intelligent Monitoring in Intensive Care (MIMIC-III) database, 8243 adult patients who underwent cardiac surgery were included. The association between MHR and the 30-day, 90-day, 180-day, and 1-year mortality of patients undergoing cardiac surgery was analyzed using multivariate Cox proportional hazard analysis. As a continuous variable, MHR was evaluated using restricted cubic regression splines, and appropriate cut-off points were determined. Kaplan–Meier curve was used to further explore the relationship between MHR and prognosis. Subgroup analyses were performed based on age, sex, hypertension, diabetes, and ethnicity. The rates of the 30-day, 90-day, 180-day, and 1-year mortalities of patients in the low MHR group were higher than those in the high MHR group (4.1% vs. 2.9%, P < 0.05; 6.8% vs. 5.3%, P < 0.05; 8.9% vs. 7.0%, P < 0.05, and 10.9% vs. 8.8%, P < 0.05, respectively). Low MHR significantly correlated with the 30-day, 90-day, 180-day, and 1-year mortality after adjusting for confounders. A U-shaped relationship was observed between the 30-day, 90-day, 180-day, and 1-year mortality and MHR, and the mortality was lowest when the MHR was 69 bpm. Kaplan–Meier curve analysis also indicated that low MHR had poor prognosis in patients undergoing cardiac surgery. According to subgroup analyses, the effect of low MHR on post-cardiac surgery survival was restricted to patients who were < 75 years old, male, without hypertension and diabetes, and of White ethnicity. MHR (69 bpm) was associated with better 30-day, 90-day, 180-day, and 1-year survival in patients after cardiac surgery. Therefore, effective HR control strategies are required in this high-risk population.