The bioavailable mercury (Hg) in the soil is highly active and can affect the formulation of methyl-Hg (MeHg) in soil and its accumulation in rice. Herein, we predicted the concentration of MeHg in rice using bioavailable Hg extracted from soils; additionally, we determined the threshold value of soil Hg in karst mountain areas based on species sensitivity distribution. The bioavailable Hg was extracted using calcium chloride, hydrochloric acid (HCl), diethylenetriaminepentaacetic acid mixture, ammonium acetate, and thioglycolic acid. Results showed that HCl is the best extractant, and the prediction model demonstrated good predictability of the MeHg concentration in rice based on the HCl-extractable Hg, pH, and soil organic matter (SOM) data. Compared with the actual MeHg concentration in rice, approximately 99% of the predicted values (n = 103) were within the 95% prediction range, indicating the good performance of the rice MeHg prediction model based on soil pH, SOM, and bioavailable Hg in karst mountain areas. Based on this MeHg prediction model, the safety threshold of soil Hg was calculated to be 0.0936 mg/kg, which is much lower than the soil pollution risk screening value of agricultural land (0.5 mg/kg), suggesting that a stricter standard should be applied regarding soil Hg in karst mountain areas. This study presents the threshold of soil Hg pollution for rice safety in karst mountain areas, and future studies should target this threshold range.