BACKGROUND: Heart rate variability (HRV) in patients with emotional disorders and healthy controls (HCs) has been investigated in many studies but the difference between these emotional disorders was unclear. METHODS: The PubMed, Embase, Medline and Web of Science databases were systematically searched for studies published in English that compared HCs with generalized anxiety disorder (GAD), major depressive disorder (MDD), panic disorder (PD) patients in HRV. We conducted a network meta-analysis to compare HRV in patients with GAD, MDD, PD and HCs. HRV outcomes, including time domain indices (the standard deviation of NN intervals (SDNN) and the root mean square of the successive differences between normal heartbeats (RMSSD)), and frequency domain indices (High-frequency (HF), Low-frequency (LF) and the ratio of LF to HF (LF/HF)) were obtained. A total of 4008 participants from 42 studies were included. RESULTS: The results of pairwise meta-analysis showed that compared with controls, GAD, PD and MDD patients exhibited significantly reduced HRV. Similar findings were also confirmed in network meta-analysis. The most important finding from network meta-analysis was that GAD patients had significantly lower SDNN than PD patients (SMD = -0.60, 95 % CI [-1.09, -0.11]). CONCLUSION: Our findings provided a potential objective biological marker to distinguish between GAD and PD. In the future, a large sample of research is needed to directly compare HRV of various mental disorders, which is crucial for finding biomarkers to distinguish them.