This study investigated the effects of aquatic exercise program that combination water walking exercise with a swimming exercise on body composition and a heart rate variability (HRV) modification in the middle aged obese women. The subjects of this study 20 obese middle aged women randomly selected who were in their 40s and 50s over 30% of body fat percentage, were divided into non-exercise group (n=10) and the exercise group (n=10). The exercise group was performed at 60% HRmax three times a week, and then each group aquatic exercise program carried out before and after the changes in body composition and the autonomic nervous system, the following results were observed. In the exercise group, the body weight and body fat percentage significantly decreased (p<.05) but non-exercise group increased. Changes of autonomic nervous system by HRV analysis showed that the SDDN, TP, HF significantly increased but decreased at LF in the exercise group. Whereas the RMSSD and TP a significant reduced in the non-exercise group. Consequently, This study is considered to suggest the aquatic exercise program lead to decreased sympathetic nerve activity, increased parasympathetic activity and sympathetic-parasympathetic balance due to th body weight loss and body fat percentage reduction, in obese middle aged women.