Incentive spirometry is commonly used to prevent postoperative lung atelectasis and pulmonary complications in cardiac surgery patients. However, when incentive spirometry is used clinically, patients frequently breathe by chest stretching until reminded by clinical experts to breath abdominally. This study examined the effect of different breathing methods on pulmonary function and heart rate variability in cardiac surgery patients using incentive spirometry. An experimental design was utilized for research in which 31 patients undergoing median sternotomy for cardiac surgery from two medical centers in southern Taiwan were invited to participate. Group 1 (n=16) received abdominal breathing as their incentive spirometry intervention. Group 2 (n=15) used incentive spirometry with thoracic breathing method. Both groups received three pulmonary function tests administered, respectively, prior to the operation and on the 1st and 3rd day in the general ward. Heart rate variability was measured twice per day beginning on the day before the operation and ending three days after being transferred to the general ward after receiving incentive spirometry. Data were analyzed using repeated measures ANOVA. Results showed significant interaction between time and group in the % FVC pred (F=9.233; p＜.05). Additionally, when using incentive spirometry, LF% (F=12.006; p＜.05) and LF/HF ratio (F=7.664; p＜.05) were reduced, and HF% (F=12.006; p＜.05) was enhanced during abdominal breathing as compared with thoracic breathing. The present study demonstrated optimal lung function recovery and also reflected a shift to the dominance of parasympathetic nerves regulation in using abdominal breathing rather than thoracic breathing with the application of incentive spirometry.