Abstract: The microstructure of porous media has important effect on the transport of soluble contaminants. In this paper, we use the Quartet Structure Generation Set (QSGS) to construct clay porous media with an anisotropic pore structure, and its solid particles have random rough surface. The nonuniform flow field and the concentration field in the microporous structure are calculated by coupling Stokes Equation and Advection-Diffusion Equation (ADE). We analyze the nonuniform flow field and concentration field and study the water velocity distribution at different cross-sections and explored the effect of clay's microscopic pore structure on soluble contaminant transport under the condition of the pulse injection. The results show that randomscattered pore structure is the main factor that leads to the nonuniform distribution of water velocity in flow field. Small-scale pore or dead-end pore in the clay could easily trap contaminants with high concentration, causing a 'tail' phenomenon on the breakthrough curve. Furthermore, the residual contaminant at the late time is captured in these small-scale or dead-end pores.