Magnetoencephalography (MEG) records the brain magnetic field signals. Optically pumped magnetometer (OPM) is a novel technology for MEG measurement in its infancy, it is essential to demonstrate its performance on the key neuroimaging features, such as phase-locking value. In this paper, the inter-trial phase-locking value (ITPL) and inter-region phase-locking value (IRPL) were analyzed by simulation and measurement experiments using OPM-MEG, the superconducting quantum interference device (SQUID) data was applied for the compare. The simulation results show that OPMs could offers good characterization on phase-locking value under higher noise intensity. In experiments, the similarity ratios of ITPL and IRPL between OPM-MEG and SQUID-MEG are >0.90. The significantly increased frequencies of IRPL in pure tone and somatosensory stimulation are at about 10–20 Hz and 8–13 Hz respectively, with Spearman correlation coefficients >0.7. The results provide experimental evidence of the ability of OPM-MEG for measuring phase synchronization and functional connectivity on sensor signals.