OBJECTIVE: To investigate the mechanism of interactions between autonomic nervous system (ANS) and cognitive function in Major depression (MD) with Magnetoencephalography (MEG) measurements. METHODS: Participants with MD (n = 20), and Health controls (HCs, n = 18) were completed MEG measurements during the performance of a go/no-go task. Heart rate variability (HRV) indices (SDANN, and RMSSD) were derived from the raw MEG data. The correlation analysis of the HRV and functional connectivities in different brain regions was conducted by Pearson\'s r in two groups. RESULTS: The go/no-go task performances of HCs were better than MD patients; HRV indices were lower in the MD group. Under the no-go task, a brain MEG functional connectivity analysis based on the seed regions of the orbitofrontal cortex (OFC) displayed increased functional inter-region connectivity networks of OFC in MD group. HRV indices were correlated with different functional inter-region connectivity networks of OFC in two groups, respectively. CONCLUSION: ANS is related to inhibitory and control function through functional inter-region connectivity networks of OFC in MD. These findings have important implications for the understanding pathophysiology of MD, and MEG may provide an image-guided tool for interventions.