In order to effectively decrease cadmium (Cd) in rice grains in contaminated paddy soil and maintain the safe production of rice, identifying excessive Cd in rice caused by rice varieties or soil Cd is critical, but it is currently lacking. In the present study, the soil ethylenediaminetetraacetic acid (EDTA)-extractable Cd (EDTA-Cd) and the bioaccumulation factors of rice based on EDTA-Cd (BCFEDTA-Cd) were used to develop an approach to identify excessive Cd in rice caused by rice varieties or soil Cd. Based on an empirical soil–plant transfer model and species sensitivity distribution (SSD), BCFEDTA-Cd and EDTA-Cd were divided into five grades. The results showed that the five grades of the EDTA-Cd (minimum value less than 0.11 mg/kg and maximum value greater than 2.93 mg/kg) and BCFEDTA-Cd (minimum value less than 0.09 and maximum value greater than 1.40) were classified in the normal soil pH range. Further, the conversion equation between EDTA-Cd and diethylene triamine pentaacetic acid (DTPA)-Cd was obtained through linear regression analysis using 67 sets of soil data from the literature. In addition, the four selected rounding thresholds for the percentage of EDTA-Cd to total soil Cd (EDTA-Cd) (%) were 52.5, 67.5, 82.5, and 97.5%. A selected soil EDTA-Cd (%) (about 75%) can be used to identify the status of soil bioavailability, especially in soil with high background Cd. Finally, a set of 1084 pairs of rice and soil data for Cd-contaminated soils was used to investigate the respective contributions of rice varieties and soil Cd when Cd in rice exceeds the limit (0.2 mg/kg). Based on field experiment data, a systematic identification approach for the causes of rice Cd exceeding the limit, soil Cd or rice variety, was established and applied. In conclusion, under Cd exposure conditions, the importance of the causes of Cd in soil and rice varieties can be identified, and their contributions can be distinguished, thus helping to identify the causes of Cd contamination in rice.