Usually, capillary pressure curve of sandstone is a smooth curve. However, the curve of marlstone with micro-fractures consists of two parts: an oblique line and a flat one. So the parameters such as threshold pressure and mean throat radius gained from capillary pressure curves of marlstone cannot describe the pore structure properly. This paper mainly discusses and analyzes the difference of mercury injection curves between sandstone and marlstone, and proposes a concept of effective throat radius to describe the pore structure of marlstone with micro-fracture. The case study shows this method is better than before.