The purpose of this study was to compare of physical fitness among different BMI (Body Mass Index, BMI) levels in university. The participants included 9,359 freshmen of National Formosa University from 1996 to 2011. There are assigned on six separate groups of ”underweight”(BMI<18.5), ”normal”(18.5≦BMI<24), ”overweight”(24≦BMI<27), ”obese, class 1”(27≦BMI<30), ”obese, class 2”(30≦BMI<35), ”morbidly obese”(BMI≦35). Anthropometric measures included body composition (BMI), sit-and-reach of flexibility test, sit-ups (in 30sec and one minute) of muscular strength and endurance test, standing long jump of power test, and 800M(female)/1600M(male) run-walk of cardiovascular fitness test. The results included five points: first, there are 26.71% male and 15.2% female BMI have overweight or obese. Second, male and female students have poor flexibility performance when BMI is underweight. Third, there is no significant difference of sit-ups in different female BMI groups. Male has poor performance of sit-ups when BMI was ”obese, class 2” and ”morbidly obese”. Fourth, there is significant difference of power performance when BMI is ”underweight” than ”obese, class 2” in female. There is significance difference of power performance when BMI are ”underweight” and ”normal” than ”overweight” and obesity in male. Finally, there is significant difference of cardiovascular fitness when BMI is ”underweight” or ”normal” than ”obese, class 2” and ”morbidly obese” in freshmen. High BMI had the greatest impairments in physical fitness. Therefore, the study recommended that the first goal should be to reduce the weight of freshmen and improve students' cardiovascular fitness in university.