Cardiothoracic Surgeon Salary: Factors and Influences. The average salary of a cardiothoracic surgeon ranges between $262,000 and $613,170 per year, with a median of around $417,500. This is affected greatly by the industry worked, the experience of the surgeon, and the geographic location in which the surgeon works.he average annual cardiothoracic surgeon salary is $417,500. The lowest 10% of cardiothoracic surgeon salaries are less than $262,000. The top 10% of cardiothoracic surgeon salaries reach more than $613,170.