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With the rapid economic development, the environmental pollution becomes increasingly serious. Through the analysis of causes and propagation characteristics of urban heavy metals pollution, the location of the various sources of pollution is confirmed. By using the principal component analysis model, the specific distributions of different pollutants in each area are obtained firstly. In order to ascertain the sources of heavy metal pollution, three-dimensional diffusion model between the concentration of heavy metal elements and geographic position of elements is established. With the help of the least squares method solving differential equations, the specific location of the sources of pollution is ascertained ultimately.