During the installation process of suction caisson in sandy seabed, the applied suction not only produces a downward driving force, but also decreases the penetration resistance to the caisson. In this paper, numerical studies were performed to investigate the characteristics of seepage flow around the caisson as well as its effects on the wall friction and the caisson tip resistance. A simplified approximation method was proposed to predict the reduction of penetration resistance. In particular, for the case of sandy seabed interbedded by a layer of low-permeability soil, the seepage flow will be suppressed with the caisson tip getting closer to the low-permeability layer. The seepage flow around the caisson was first studied, and then a new approximation for the seepage-induced resistance reduction, considering the effect of low-permeability layer, was proposed for the engineering practice.