Based on the study of the composition and distribution of the deep-sick cover on the river bed at a hydropower station in Jinsha River of China, this paper discusses the genetic mechanism of the cover on the dam foundation. Using a variety of theoretical formulas, the paper identifies the seepage deformation form, calculates anti-permeability strength parameters, and further comprehensively evaluates the permeability and stability of the cover. The results show that the cover on riverbed is formed by the action of the tectonic movements and the climate change, and be dominated by the climate factor. The cover has piping and flowing soil conditions, the permissible hydraulic gradient value is relatively high, and the necessary seepage prevention is needed. The conclusion provides a theoretical basis for the construction of a hydropower station.