The magnetoencephalogram (MEG) based on array optically pumped magnetometers (OPMs) has the potential of replacing conventional cryogenic superconducting quantum interference device. Phase synchronization is a common method for measuring brain oscillations and functional connectivity. Verifying the feasibility and fidelity of OPM-MEG in measuring phase synchronization will help its widespread application in the study of aforementioned neural mechanisms. The analysis method on source-level time series can weaken the influence of instantaneous field spread effect. In this paper, the OPM-MEG was used for measuring the evoked responses of 20Hz rhythmic and arrhythmic median nerve stimulation, and the inter-trial phase synchronization (ITPS) and inter-reginal phase synchronization (IRPS) of primary somatosensory cortex (SI) and secondary somatosensory cortex (SII) were analysed. The results find that under rhythmic condition, the evoked responses of SI and SII show continuous oscillations and the effect of resetting phase. The values of ITPS and IRPS significantly increase at the stimulation frequency of 20Hz and its harmonic of 40Hz, whereas the arrhythmic stimulation does not exhibit this phenomenon. Moreover, in the initial stage of stimulation, the ITPS and IRPS values are significantly higher at Mu rhythm in the rhythmic condition compared to arrhythmic. In conclusion, the results demonstrate the ability of OPM-MEG in measuring phase pattern and functional connectivity on source-level, and may also prove beneficial for the study on the mechanism of rhythmic stimulation therapy for rehabilitation.