Cadmium (Cd) threatens rice quality and human health, yet this risk remains uncertain in paddy fields with high geological background of transportation and deposition. In this study, we collected 31 pairs of soil and rice grain samples in Doumen and Xinhui Districts in Guangdong province, China and investigated which factors controlled Cd bioavailability in soil and accumulation in rice. Soil samples were mostly acidic and contained a range of organic matter. Total Cd in soil varied from 0.10 to 1.03 mg kg^− 1 and was positively correlated with those of calcium (Ca), manganese (Mn) and iron (Fe), suggesting that these elements shared same sources and Cd was most likely originated from parent material. The activity ratio (AR, CaCl₂-extractable Cd/soil Cd) and bioconcentration factor (BCF, rice grain Cd/soil Cd) of Cd were negatively correlated with soil pH. The coupling relationship between soil and rice grain Cd could be described by a linear model, which was used to predict soil Cd threshold values to keep rice grain Cd concentration from exceeding the Chinese limit (0.2 mg kg^− 1). In summary, Cd pollution was not very severe in the paddy soils of studied area but the risk could not be neglected when soil was acidified, which could increase Cd bioavailability and accumulation in rice grain.