Coupling analysis of seepage and stress has attracted considerable attention in numerical simulation. The influence of seepage on stress is reflected in the seepage load. Nevertheless, there are two decided differences listed below when scholars deal with the water pressure and boundary conditions with ABAQUS software: whether it is necessary to apply hydrostatic pressure when pore pressure boundary is defined; and whether it is essential to define uplift pressure on dam foundation if the seepage field of foundation rock is considered. In view of this, we analyzed the two problems based on vertical stress balance and pore hydrostatic pressure balance theories as well as numerical examples, and conclude that both hydrostatic pressure and pore pressure boundary should be considered when submitting coupled process of seepage and stress with ABAQUS software. Moreover, uplift pressure should be applied when the permeability of dam body is not considered; but when the permeability of dam body is taken into consideration, uplift pressure is not required anymore. The results offer reference for the application of ABAQUS software to seepage-stress coupling analysis of concrete gravity dam.