Determining the safety threshold of heavy metals in soil is an important measure to ensure the quality and safety of agricultural products in China. By studying the accumulation and transportation characteristics of five heavy metals (Cr, Cd, Pb, As, and Hg) in different organs of corn and wheat in the cities of Jinchang, Zhangye and Baiyin in Gansu Province and establishing the relationship between the effective content of Cr, Cd, Pb, As, and Hg in soil and crop grains, this study identified the safety threshold of effective heavy metals in soil for corn and wheat systems. This study employed the method and principles of species sensitivity distribution (SSD) and derived the safety threshold of effective heavy metals in soil for corn and wheat planting systems based on the cumulative probability distribution curve of the Logistic function distribution model. The results showed that the accumulation pattern of Cr, Cd, Pb, As and Hg in wheat plants was consistent, namely, roots>stems>grains, and similarly, the accumulation pattern of Cr, Pb, As and Hg in corn plants was roots>stems>grains, while the accumulation pattern of Cd was stems>roots>grains. Utilizing the Logistic function distribution model to fit the cumulative probability distribution curve based on the effective content of heavy metals, the safety thresholds of effective Cr, Cd, Pb, As and Hg in wheat soil were determined to be 0.019, 0.771, 35.294, 2.777 and 0.133 mg/kg, respectively. Meanwhile, the safety thresholds of effective Cr, Cd, Pb, As and Hg in corn soil were determined to be 0.296, 7.90, 52.363, 12.462 and 0.119 mg/kg, respectively. The results of this study indicate that estimating the safe threshold of effective heavy metal content based on the cumulative probability distribution curve method was scientific, providing a scientific basis and support for the safe planting and risk control of wheat and corn.