A probabilistic environmental quality assessment method of soil heavy metals based on Monte-Carlo simulation and index of geoaccumlation was developed by considering the data screening and weighting system of different heavy metals' biology-toxicity. Then, a case of contaminated farmland soil was put forward to test and verify the feasibility of the proposed method. Then, by building the factor probability distribution models of the sample content parameters and corresponding background value parameters, the probabilistic quality assessment method was applied with the preferences of maximum number of trials 1000, confidence level 95% and Latin hypercube sampling method. The results showed that the pollution degrees of these heavy metals were in the order Cd＞Ni＞Zn＞Cu＞Cr. The pollution degree of Cd belonged to the probability of serious pollution level as high as 98.1%. Ni and Zn were in spatial distribution of a clear difference, and belonged to the probability of serious pollution level at 84.5% and 87% respectively. Cu and Cr were relatively low in pollution level. At last, through a comparative analysis, the results showed that the proposed method owned a higher resolving property, and could express their corresponding probabilistic risk levels, which provided a basic theory to scientific decision-making.