To observe the effect of sacral nerve stimulation (SNS) on the autonomic nervous function in patients with chronic functional constipation. Eighty-six cases of chronic functional constipation patients in Xijing Digestive Hospital and the Mayinglong Coloproctological Hospital of Xi′an from September 2016 to November 2017 were randomly divided into two groups, forty-two cases in the treatment group and forty-four in the control group. The treatment group was treated by non implantable sacral nerve stimulation treatment, and the control group was treated by acusector treatment at baliao acupoint. Constipation symptom score and heart rate variability were measured before and after treatment between the two groups. The results showed that the scores of constipation symptoms in the two groups were decreased (P<0.05). The changes of HRV in the treatment group were significantly different (HF: u=-2.269, P=0.023; LF: u=-5.183, P=0.000; LF/HF: u=-4.359, P=0.000), and there was no effect in the control group. There were no statistical difference between the two groups on the comparison of constipation symptoms scores and HRV indexes before and after treatment (P>0.05). There were statistical difference on concomitant symptom score difference values (t=4.040, P=0.000) and the HRV difference values (ΔHF: u=-2.583, P=0.010; ΔLF: u=-5.089, P=0.000; ΔLF/HF: u=-3.299, P=0.001). SNS may improve the function of chronic functional constipation by influencing autonomic nerve function.