With the gradual emphasis on health by people, the research on the pathogenesis of endemic diseases has become increasingly in-depth. Through analyzing the environmental selenium characteristics and conducting a comparative study in typical areas of Chinese loess and black soil in this paper, it is concluded that the environmental selenium in the two regions has different characteristics. The soil in the loess area has the characteristics of high alkalinity, low selenium, and relatively high selenium availability, and the crops are selenium-deficient, while the soil in the black soil area has the characteristics of high organic matter, low selenium availability, and relatively high selenium in crops. The research concluded that the environmental occurrence mechanism of Keshan disease in the loess area and the black soil area is different. Keshan disease can be induced in both low-selenium and sufficient-selenium environments, and environmental selenium should be one of the inducing factors of Keshan disease. This research provides a reference for predicting the areas where Keshan disease occurs and for disease prevention, and it can also serve in the prevention and control of endemic diseases.