Abstract: By testing data obtained from the Yantai eco-geochemical survey and associated special topic study, it was discovered that Cd, Hg, Pb, As and other heavy metal elements' geochemical mechanism influence activation and migration in the acidic soil environment of a heavily metal-polluted area, as well as indicating the reason for ecological risk of heavy metal in shallow underground water and main grain seeds. Compared with the reference and background values of the whole country's soil, Cd, Cr, Ni and Pb's reference values in this study area were relatively high, and the background values of Cd, Cr, Pb, Cu and Ni were relatively high. As, Cd, Cr, Ni, Hg and Pb occurred in the three-grade and above three-grade soil, which were the main pollutants. Heavy metal elements, which exceed the standard, were detected in shallow groundwater from typical gold contaminated areas and corn fruits. Pb is the main index that affect the quality of shallow groundwater. The number of three-grade and above three-grade water samples was 30, which accounted for 3.47% of the total sampling points. There were 4 corn samples in which the Cd content was higher than the agricultural contamination standard, which account for 12.9%. The comparative study indicates that surface acidic soil accounts for the total soil area acidity increasing from 16.04% to 55.29%. The soil acidic trend is obvious. As the soil acidification was worse in the depth and coverage area, the soil ecological environment had deteriorated, which led to the loss of nutrient elements and some poison elements (Cd, Pb) being released and activated. It also raised the heavy metal elements' activity and migration ability, such as Cd, Hg, Ni, Pb and As. Soil rich in SOM helped to absorb heavy metal elements, such as Cu, Zn, Pb, Cd, and reduced the environmental risk level of soil heavy metal pollution. This provided a scientific basis for restoring the soil and reducing the toxicity of the soil.