Abstract: Hakanson comprehensive index method is one of the methods for the potential ecological risk assessment of heavy metals in contaminated soil. Although its effectiveness has been proved, there also exist several disadvantages. Firstly, the difference in the toxicity of each fraction of heavy metals is ignored. Secondly, it is applied to the case that heavy metal content is higher than the background value, while for the opposite case it is not suitable. As a result, the Hakanson comprehensive index can hardly reflect the real risk in some cases. To solve these problems, the authors tried to modify Hakanson comprehensive index method on the basis of the theory of the whole process control and optimization. The Xiaoqinling gold mining area, which is located in eastern Shaanxi Province and is the second largest gold mining area in China, was selected as a case study. The modified Hakanson comprehensive index method was checked, and the results show that the modified method is effective for potential ecological risk assessment, and hence has a greater adaptability.