The invention discloses a site contaminated soil distribution determination method based on geological conditions. The method includes the following steps: 1) collecting the geological parameters of a to-be-tested site, comprising: soil geologic stratification, soil layer permeability, soil granular size, soil organic substance content, and water level, flow direction and flow speed of underground water, and determining the background values of the parameters; 2) collecting the environmental data of the site to determine the types of the pollutants; 3) determining investigation depth according to the types of the pollutants and the soil layer permeability coefficient; and 4) determining investigation zones according to the soil layer permeability coefficient, the soil organic substance content, and the water level, the flow direction and the flow speed of underground water. The method, on the basis of the character analysis of geological conditions, can be used for macroscopically determining and investigating the characters of distribution and migration of local soil pollutants with combination of the environmental data through various test methods. The method is low in workload, is short in period and is low in cost. A diagnosis result can effectively guide arrangement of sampling points and determination of sampling depth in site environment investigation in later period.