Increasing numbers of cardiothoracic surgery residents are resigning, without completing their training. This study analyzes how their turnover intention is related to the training environment, and individual psychological factors. Responses by 57 Korean cardiothoracic surgery residents were analyzed. Their levels of depression, anxiety, grit, and empathy, working conditions, the effect of someone’s presence to discuss their concerns with, burnout, and turnover intention were identified as the research variables. Descriptive statistical analysis, correlation analysis, and structural equation modeling were used for data analysis. Burnout has the most significant relationship with turnover intention. It has a mediating effect on the influence of depression, grit (sustained interest), and working conditions, over turnover intention. Empathy, and the presence of someone to discuss concerns with, also affect turnover intention directly. The study also confirmed that grit and work satisfaction affect turnover intention indirectly, through burnout. The study identified both individual- and systemic-level factors for an effective training environment, to reduce cardiothoracic surgery residents’ tendencies of leaving the residency program, and supporting them for greater satisfaction with their career choice. In order to resolve negative emotions such as burnout and depression, and foster empathy, a human resource development program for the residents’ psychological support must be prepared. The program director should be adequately educated to take charge of the training program, oversee the residents’ education and welfare, and perform the roles of role-model and mentor.