Focused supervision and early warning of heavy metal (HM)-contaminated rice areas can effectively protect people’s livelihood security and maintain social stability. To improve the accuracy of risk prediction, an Informer-based safety risk prediction model for HMs in rice is constructed in this paper. First, based on the national sampling data and residential consumption statistics of rice, we construct a dataset of evaluation indicators that can characterize the level of rice safety risk so as to form a safety risk space. Second, based on the K-medoids clustering algorithm, we classify the rice safety risk space into levels. Finally, we use the Informer neural network model to predict the safety risk indicators of rice in each province so as to predict the safety risk level. This study compares the prediction accuracy of a self-constructed dataset of rice safety risk assessment indicators. The experimental results show that the prediction precision of the method proposed in this paper reaches 99.17%, 91.77%, and 91.33% for low, medium, and high risk levels, respectively. The model provides technical support and a scientific basis for screening the time and area of HM contamination of rice, which needs focus.