To explore the irrigation mode to effects of heavy metals on brown rice, paddy soil, and rice yield, we selected a moderately heavy metal polluted paddy soil from Pingxiang district of Jiangxi province in China. In comparison with the traditional intermittent irrigation, the rice yield decreased about 1.25% under long-term flooding irrigation. The contents of Cd, Pb and Cr in brown rice decreased approximately 42.79%, 3.70% and 44.81%, respectively. The contents of Hg and inorganic As in brown rice increased about 200% and 3.29%, respectively. The content of Cd in paddy soil decreased approximately 38.77%, while the content of available Cd and cation exchange capacity significantly decreased 72.08% and 36.71%, respectively. Interestingly, the pH and the content of organic content in paddy soil increased 0.97% and 6.32%, respectively. The correlation analysis indicated that there was a significant negative correlation between the available Cr level in brown rice and soil organic content, while positive correlation between Cr content in brown rice and cation exchange capacity in paddy soil. The content of Hg in brown rice was significantly and negatively correlated with the available Cd level and cation exchange capacity in paddy soil. This work indicate that the long-term flood irrigation in contaminated paddy soil can effectively reduce the available Cd level in the rice, but result in the increase of Hg accumulation, and the decrease of rice yield in comparison with traditional intermittent irrigation mode.