Paddy crusts (PCs) influence seriously on the heavy metal migration and transformation in the paddy field system. However, their quantitative effect on heavy metal accumulation in rice plant has been rarely reported. In this study, the influence of microcystis-dominated PCs on Cd content and physicochemical properties of the surface soil, water and rice plants (Oryza sativa L.) during PCs' overall life cycle was investigated. During the PC growth period (0–15 d), the Cd content in the surface soil (0–10 cm) and water decreased by 10–20% due to the accumulation effect. However, during the perish period (15–35 d), the Cd content in the surface soil and water increased by 20–30%, as Cd stored in the PCs was re-released. Moreover, the decomposition of PCs produced a large amount of low-molecular-weight organic substances (<500 Da), significantly increasing the bioavailable acid-soluble Cd in the surface soil. Finally, the PCs increase 25–80% and 60–85% Cd content in rice root and shoot, respectively. A structural equation model demonstrated that the contribution to the Cd in rice roots in the sequence: Cd in surface water > PC > surface soil. Potted experiments using sandy, clay, sandy loam soil containing 0.8–3.5 mg/kg of Cd collected from six provinces’ paddy field in southern China confirmed that PCs increased the Cd accumulation in rice plants by as much as 25–80%. Consequently, the presence of PCs can enhance the Cd concentration in rice plants, and the removing PCs could be a potential effectively approach to reducing Cd content in rice plants.