Objective. The present study examined the effects of a 12-week whole-body vibration training (WBVT) regimen on heart rate variability (HRV) and body composition in the obese female college students. Methods. Participants were assigned to either the WBVT (
n
=
17
) or obese control group (
n
=
19
). The students in the WBVT group conducted a 12-week (5 times per week and 30 min per time) exercise protocols (30 to 40 Hz of frequency and 4 mm of amplitude), and the obese control group did not perform regular physical training during 12 weeks of study. Then, body composition (body weight, BMI, body fat, body fat percentage; trunk fat mass, muscle mass, MM) and HRV (time domain and frequency domain index) were measured in all subjects before and after WBVT intervention. Results. (1) After 12-week WBVT intervention, body fat mass, trunk fat mass, and body fat percentage significantly decreased and muscle mass increased in the WBVT group (
P
<
0.01
, respectively); there was no significant change in body weight and BMI (
P
>
0.05
, respectively). (2) After 12-week WBVT intervention, LFn, LF/HF, and HR significantly decreased (
P
<
0.05
,
P
<
0.01
), R-R interval and RMSSD significantly increased (
P
<
0.01
, respectively), and there was no significant difference in HFn (
P
>
0.05
). Nevertheless, there was no significant change before and after the test in body composition and HRV in the obese control group (
P
>
0.05
, respectively). (3) After 12-week WBVT intervention, compared with the obese control group, body fat mass, body fat percentage, trunk fat mass, and LF/HF significantly decreased (
P
<
0.05
,
P
<
0.01
), muscle mass, and RMSSD increased (
P
<
0.05
) in the WBVT group; but there were no significant difference in other indicators (
P
>
0.05
) between the obese control group and WBVT group. (4) The reduction of body fat percentage before and after the WBVT intervention are positively correlated with the reduction in the LFn and LF/HF (
r
=
0.542
,
r
=
0.504
;
P
<
0.05
, respectively) and negatively correlated with the increase in the RMSSD (
r
=
−
0.514
,
P
<
0.05
), and the reduction of trunk fat mass are positively correlated with the reduction in the LF/HF (
r
=
0.540
,
P
<
0.05
). Conclusion. The results indicate that WBVT improves HRV and body composition in obese female college students, and the reduction in body fat percentage and trunk fat mass are associated with a shift in cardiac autonomic regulation towards vagal dominance and improve sympathetic-vagus balance after WBVT intervention. In conclusion, WBVT may be a feasible treatment to improve cardiac autonomic function and body composition.