The ecological and health risks caused by heavy metals (HMs) have become a global challenge. In Jinhua, China, four kinds of irrigation water sources (primary and secondary treated water R1 and R2 of rural domestic sewage, purified water R3, and river water (CK) and three kinds of water level regulations (low, medium and high water level control of W1, W2 and W3) were set to study the impact of rural domestic reclaimed water (RDRW) irrigation on the distribution and migration of HMs in soil, plants, and groundwater. The HM content in RDRW met the standards for irrigation water quality, compared to CK, under RDRW irrigation, the Cd and Zn contents in rice fields increased, while the Cr and Pb contents decreased, the impact of irrigation water sources on the HM content was gradually weakened along the direction of stems, leaves, and grains, and the groundwater has not been contaminated. Additionally, the migration ability of HMs from the soil to rice plants was not significantly affected, soil's ability to reduce HMs was enhanced, with a reduction rate over 96% for Zn, Cr, Cu, and Cd, and the rice grains showed moderate uptake of Zn and Cd, weak uptake of Cr and Cu, and extremely weak uptake of Pb. Under RDRW irrigation, oral-crops were the main risk exposure pathway, with adults and children accounting for 60.92% and 63.61% of the total individual annual risk, respectively, and Cd contributed the most to the total individual annual risk, and it was the main HM element causing health risks. It is recommended to strengthen the monitoring and prevention of Cd accumulation in reclaimed water irrigation areas.