Methylmercury (MeHg) in rice is presumed to be derived from MeHg formed in the soil, although it is still controversial. Moderate soil mercury (Hg) concentration can affect the diversity of soil microorganisms and may also impact the physiological changes and MeHg absorption of rice. In this study, the pot experiment was conducted to explore the effects of Hg concentration gradients (0, 0.3, 3, and 30 mg kg−1) stress on Hg transformation in the rhizosphere, Hg translocation in rice, and physiological changes in rice leaves during the whole rice growing season. Moderate soil Hg concentration (3 mg kg−1) greatly increased the MeHg/THg (1.69%) of rhizosphere, while 30 mg kg−1 soil Hg concentration sharply reduced the MeHg/THg (0.29%) of rhizosphere. Highest MeHg/THg of the four groups all appeared at the blooming or filling stage. There was a significant positive correlation between Fe2+ in rhizosphere and MeHg/THg, but no significant correlation between SO42− and MeHg/THg was observed. Although the 3 mg kg−1 soil Hg concentration significantly enhanced MeHg concentrations in seeds, it considerably reduced the bioaccumulation factors of MeHg in roots, stalks, old leaves and young leaves. Soil Hg concentration of 30 mg kg−1, to a certain extent, curtailed MeHg concentrations in seeds, while MeHg concentrations in the husk were significantly increased. Consistent with the result that there was no significant difference for THg concentrations in old and young leaves among the four Hg treatment groups, the content of chlorophyll, H2O2, malondialdehyde and antioxidant substances, and the activities of antioxidant enzyme in old and young leaves varied indistinctly among groups. Main findingModerate soil mercury concentration (3 mg kg−1) could extremely enhance MeHg production in the rhizosphere soil and its accumulation in rice; MeHg production in the rhizosphere soil increased greatly at the blooming or filling stage, whereas little effect on antioxidant systems in leaves was observed.