Determination of main impact factors of river health is important to river management, ecological rehabilitation and construction. Based on the definition of river health in China, the factors were divided into two categories, that is, endogenous factors and exogenous factors. The method used to main impact factor analysis was suggested which is based on the relation between the factors and the partial least squares regression. The model was applied to analyze main impact factors of river health of the lancun-Yitang reach in the middle Fenhe River. The result shows that the proposed model can reflect the actual situation.