In order to find a combination of geochemical elements reflecting the abnormal mineralization, this paper provides a method of structural equation modeling（SEM）for geochemical data processing based on principal component analysis（PCA）. This study not only describes the principle of structural equation modeling, but also makes use of it in the geochemical data analysis experiment. The geochemical data is measured from lake sediments samples obtained from the Southwest Nova Scotia, Canada; a model of geochemical elements related to the hydrothermal fluid gold mine is established. The results shows that the factor variables related to the gold mine computed by the structural equation modeling are highly correlated to the space of the gold deposits, and they can also better predict the gold deposits.