Black fungus is the second-most consumed edible fungus in China. The establishment of a risk assessment mechanism for heavy metals in black fungus is particularly critical to the safety of edible fungi. To clarify a risk assessment mechanism of heavy metal pollution of edible fungi in northeast China, in this study, the contents of Pb, Cr, CD and As in 415 samples were determined, and a total of 1660 valid data were obtained. Then, based on Monte Carlo simulation, a non-parametric probability assessment system for heavy metals in black fungus was established and improved. The results showed that the residual amounts of As, Pb, Cd and Cr in black fungus were in the order of Cr > Pb > As > Cd. The background content of four heavy metals in the main raw materials was preliminarily clarified. Among them, the content of As is between 0.010–0.320 mg·kg−1, Pb is between 0.051–0.792 mg·kg−1, Cd is between 0.019–0.236 mg·kg−1, and Cr is between 0.06–3.41 mg·kg−1. These results indicate that the dietary exposure risk of heavy metals ingested by dried black fungus in Chinese minors and adults is basically safe, but at the high exposure levels of 97.5% sites and 99% sites, Cr is at the light pollution level, and the comprehensive pollution of four heavy metals is at the moderate pollution level. In addition, this study found that raw materials can cause heavy metal accumulation in black fungus, mainly from sawdust, followed by rice bran and wheat bran.