Cadmium (Cd) contamination in soil-rice systems has become a global public concern. However, influencing factors and the contamination threshold of Cd in soils remain largely unknown owing to soil heterogeneity, which limits our ability to assess the risk to human health and to draft appropriate environmental policies. In this study, we selected the soil-rice system of Longtang and Shijiao town in southern China, which was characterized by multi-metal acidic soil contamination due to improper electronic waste recycling activities, as a case to analyze the influence of different soil properties on the Cd threshold in the soil and Cd accumulation in rice. The results showed that soil organic matter (SOM) was the main factor regulating Cd accumulation in the soil-rice system. Moreover, compared with the total Cd concentration, the DTPA-extractable Cd concentration in the soil was a better predictor of Cd transportation in the soil-rice system. According to the prediction model, when SOM was < 35 g kg^-1, the Cd_DTPA threshold was 0.16 mg kg^-1 with a 95% likelihood of Cd_rice accumulation above the Chinese food standard limit (0.2 mg kg^-1). Conversely, when SOM was ≥ 35 g kg^-1, the Cd_DTPA threshold was only 0.03 mg kg^-1. This study of the influence of SOM on Cd accumulation in a soil-rice system confirms that SOM is a crucial parameter for better and safer rice production, especially in multi-metal contaminated acidic soils.