Objective To observe the influence of swimming exercise at different intensities on heart rate variability of adult with metabolic syndrome (MS) in quiet condition. Methods A total of 126 adults with MS were divided into the low intensity exercise group, the moderate intensities of exercise group and the high intensity exercise group. All groups were given different intensities of swimming exercise training for 4 weeks,and the HRV indexes were compared between before and after exercise. Results The LF were reduced on the training instantaneousness, and rose slowly in 30 min of recovery time in the three groups, and the most obviously rising group was the high intensity exercise group (P < 0.05). HF increased in the low intensity exercise group, and reduced in the moderate and high intensity exercise group on the training immediately(P < 0.05). The SNDD reduced on the training immediately, and rose slowly on recovery time of 30 min in the three groups, but there was no statistically significant difference between the groups (P > 0.05). The RMSSD rose on the training immediately in the three groups, and in 30 min of recovery time the RMSSD rose slowly in the three groups. The PNN50 reduced on the training immediately in the three groups, and in 30 min of recovery time, the PNN50 rose slowly in the moderate and high intensity exercise group, and reduced in the low intensity exercise group (P < 0.05). LF, HF, RMSSD and PNN50 rose and LF/HF reduced significantly after exercise in the moderate and high intensity exercise group compared with the low intensity group (P <0.05 orP < 0.01). Conclusions The moderate and high intensity swimming exercise training can improve HRV in adults with MS, but there is no significant effect of low intensity swimming exercise training on HRV.