Substrate, which not only takes part in the pollutant-removing, but influences the plant growth, plays an important role in subsurface flow wetland. With X-ray fluorescence measurement and X-ray diffractometer, the elements and minerals in zeolite and shale were confirmed, and the removal mechanics of nitrogen, phosphate and hydrogen ion in substrates were explained respectively. The investigation show that the zeolite has abounded with micropores and mesopores, while the shale has only mesopores, which causes the NH4+ -N adsorption capability of the shale is less than zeolite. The PO4(3-) -P removal and hydrogen ion buffer capacity of shale are greater than those of zeolite because CaCO3 is one of the main contents of shale. In pilot-plant system to treat starch waste water, the reeds and acorus aclamuc were either planted in shale and zeolite, and the phytum's indexes in shale including relative green concentration, average plant height, root stem ratio were higher than those in zeolite. The root vitality of reeds and acorus aclamuc planted in shale were 3.7 and 1.6 times of those in zeolite respectively. Total nitrogen and phosphorus contents in the plant organization of acorus aclamuc in shale were 7.8 and 3.4 times of those in zeolite; total nitrogen and phosphorus contents in the plant organization of reeds in shale were 3.3 and 2.2 times of those in zeolite. The results indicate that shale provides a steady pH for the plant's root in the acid waste water and it is more suitable for plant growth than zeolite.