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Cadmium (Cd) pollution in a soil–rice system is closely related to widely concerning issues, such as food security and health risk due to exposure to heavy metals. Therefore, modeling the Cd content in a soil–rice system and identifying related controls could provide critical information for ensuring food security and reducing related health risks. To archive this goal, in this study, we collected 217 pairs of soil–rice samples from three subareas in Zhejiang Province in the Yangtze River Delta of China. All soil–rice samples were air-dried and conducted for chemical analysis. The Pearson’s correlation coefficient, ANOVA, co-occurrence network, multiple regression model, and nonlinear principal component analysis were then used to predict the Cd content in rice and identify potential controls for the accumulation of Cd in rice. Our results indicate that although the mean total concentration of Cd in soil samples was higher than that of the background value in Zhejiang Province, the mean concentration of Cd in rice was higher than that of the national regulation value. Furthermore, a significant difference was detected for Cd content in rice planted in different soil groups derived from different parental materials. In addition, soil organic matter and total Cd in the soil are essential factors for predicting Cd concentrations in rice. Additionally, specific dominant factors resulting in Cd accumulation in rice planted at different subareas were identified via nonlinear principal component analysis. Our study provides new insights and essential implications for policymakers to formulate specific prevention and control strategies for Cd pollution and related health risks.