Abstract: The deep low permeability layers in earth-rock cofferdam foundation often need to use the treatment measures such as gravel piles to shorten the distance between consolidation drainages to control the cumulative quantitiy of the excess pore water pressure and to speed up its dissipation rate so as to reduce the deformation of dam foundation and improve the security of the seepage control system and stability against sliding of the dam foundation. Based on the needs of the design demonstration and optimization of the upstream cofferdam of Lava Hydropower Station, the 2D and 3D finite element simulation methods for the coupling of seepage and stress deformation in the whole process of cofferdam filling and foundation pit excavation are developed and implemented in the software LinkFEA, and are successfully used in the calculation and analysis of the cofferdam. The coupled simulation method for seepage and deformation of saturated soil foundation including gravel piles and its key simulation techniques are introduced, and the simulation of soil filling in water and construction of cutoff wall and gravel piles in the coupled calculation as well as the simulation of the permeability coefficient of low permeable soil layers changing with the compaction is realized. The pore water pressure and displacement at two typical stages are analyzed, and the variation characteristics of pore water pressure, stress and displacement are described.