Electric charges exist on the clay particle surfaces and induce a micro-electric field which leads to the formation of adsorbed water surrounding clay particles and exerts an influence on the movement pattern of ions in pore water, resulting in the ion effect of seepage in clay. The two factors above will obviously change the characteristics of seepage in micropore of clays. The change of seepage property caused by the factors mentioned above is defined as micro-electric field effect on seepage (MEFES) in clay. The electric potential on the surface of micro particles of clay amounts to tens or hundreds of mV, and then the electric field on the particle surface greatly affects the regulation of seepage. Using theoretical analyses, MEFES in micro particle clays is discussed in this paper. A theoretical model of seepage is proposed for the quantitative description of MEFES. The theoretical model shows the influences of particle surface electric potential, pore sizes, soil conductance, ion concentration in pore water, ion valence , viscosity etc. on seepage characteristics. The equivalent permeability coefficient derived from the theoretical model can be also simplified to that of Darcy’s law without regard to MEFES.