In this study, 302 samples of rice grains and 97 samples of vegetables in the farmlands in Southern Jiangsu were collected in 2019 and 2020 and the health risks of cadmium (Cd) and mercury (Hg) in the edible portions of the plants were evaluated. The results showed that Cd and Hg concentrations in rice grains were greater than those in vegetables. The mean concentrations of Cd in rice grains and vegetables were 59.5 and 50.7 μg/kg, respectively, and 4.6% and 4.1% exceeding the national standards of China. The mean concentrations of Hg were 4.7 and 0.7 μg/kg, respectively, and 3.3% and 0% exceeding the national standards of China. The estimated daily intake (EDI) of Cd and Hg in rice grains and vegetables were 0.371 and 0.239 μg/kg, and the total hazard quotient (THQ) of rice grains and vegetables was 0.680 (lower than 1), indicating that the health risk of local crops was low. The accumulation differences of Cd and Hg in edible portions of different crop cultivars were further compared, Japonica rice and root vegetables accumulated less Cd in edible portions when compared to Indica rice and leaf vegetables, respectively. Cultivating and consuming more grains from Japonica rice and root vegetables are recommended in order to decrease the potential health risk from Cd and Hg pollution and thus to alleviate the health risk from local crops.