Biochar is a potential amendment for the remediation of Cd-contaminated soils. Although the immobilization effect of biochar on soil Cd has been studied under indoor laboratory conditions, the effect of biochar on rice Cd uptake and soil Cd fractions under field conditions is still poorly understood. Here, the Cd content of the different organs of rice and the Cd fractions in soil were characterized for three years after the application of different amounts of biochar (0, 7.5, 15, 30 t ha−1, and 3 t ha−1 year−1). The Cd content of brown rice, husk, leaf, stem and sheath, and root under biochar treatment could be maximally reduced by up to 26.25%, 20.16%, 20.74%, 33.2%, and 26.89%, respectively. Biochar altered the Cd fractions in soil, including the decrease in exchangeable Cd content and the increase in Fe-Mn oxide bound Cd and organic bound Cd. The concentration factor of Cd uptake by rice was reduced by 32% under biochar application, while biochar had little influence on the transfer factor and distribution factor. The immobilization effect of biochar on soil Cd lasted for at least three years, but the trend of Cd immobilization efficiency over time for different amounts of biochar treatment was different. The Risk Assessment Code (RAC) of Cd in soil with biochar amendment could be reduced to a medium risk level from a high risk level. Redundancy analysis (RDA) revealed that changes in soil pH and Fe-Mn oxide bound Cd content caused by biochar application contributed most to the reduction in the Cd content of rice organs. These findings would enhance our understanding of the immobilization effect of biochar on Cd in paddy soil under field conditions.