The aim of this study is to form the sulfur defects on monolayer molybdenum disulfide (MoS2) by low temperature microwave plasma treatment suppressing disturbance of molecular structure. CVD-grown and plasma treated multilayer MoS2 surface were analyzed to investigate the effects of H2 and Ar plasma treatment on sulfur defects and molecular structure. It was found that the disturbance of molecular structure was suppressed in the H2 plasma treatment compared to the Ar plasma treatment. Varying the incident ratio of hydrogen ions H+ and radicals H*, the influences of H2 plasma treatment with high and low H*/H+ ratio on monolayer MoS2 structure were discussed. As a result of X-ray photoelectron spectroscopy, Raman spectroscopy and photoluminescence analysis, sulfur defects increased with the increase in total amount of radical incident on MoS2. In addition, it is speculated that the etching with radical contributed to form sulfur defects suppressing the disturbance of molecular structure.