The autonomic nervous system (ANS) maintains homeostasis in the gastrointestinal tract, including immunity, inflammation and motility, through the brain-gut axis. To date, the associations between ANS function and inflammatory bowel disease (IBD) have been controversial and inconclusive in human studies. PubMed, Cochrane Library, and Embase were searched through February 2020 for articles reporting these association between heart rate variability (HRV), an indirect measure of ANS activity, and IBD. The standardized mean differences and 95% confidence intervals (CIs) were calculated. Ten eligible studies involving 273 ulcerative colitis patients, 167 Crohn's disease patients and 208 healthy controls were included. The values of the total power (SMD = -0.83, 95% CI = -1.44, -0.21), high frequency (SMD = -0.79, 95% CI = -1.20, -0.38), RR interval (SMD = -0.66, 95% CI = -1.04, -0.27), standard deviation of the RR intervals (SMD = -1.00, 95% CI = -1.73, -0.27), percentage of RR intervals with a greater than 50-millisecond variation (SMD = -0.82, 95% CI = -1.33, -0.30) and the square root of the mean squared differences in successive RR intervals (SMD = -0.71, 95% CI = -1.15, -0.26) of the IBD patients were lower than those of the healthy controls, and moderate to large effect sizes were observed in all HRV indices, except for low frequency (SMD = -0.41, 95% CI = 0.95, 0.13). IBD was strongly associated with an overall decrease in HRV, indicating substantially decreased ANS activity. Furthermore, the parasympathetic nerve displayed a stronger inverse association with ANS activity than the sympathetic nerve, indicating ANS dysfunction in patients with IBD.