Anti-permeability, durability even strength of cement-based composites are closely related with the material pore structure. Polyvinyl alcohol (PVA) fiber reinforced strain hardening cement-based composites (SHCC) are provided with high ductility and multi- micro-crack propagation mode. Due to fibers adding, much more interface and tiny fracture had been drawn into SHCC, although it has some advantages such as high tensile strength, ductility and energy consumption under seismic load or other cyclic force. Water repellent treatment can improve the anti-permeability of SHCC. Investigations have been made through Mercury injection experiment to reveal influence on microstructure of PVA-SHCC by silane water repellence. Results show that, the pore structure of SHCC can be fined by inside water repellent agent. That is, water repellent infiltrate through the relative big hole or defect of cement paste and react with the alkali substance. Then the resultant colloids reduce the big hole, pore or fracture and reform the pore structure of the cement paste. Because the fine pore structure can prevent air, water and ions defuse into interior of cement-based composites, water repellent treatment is benefit to increase anti-permeability of high ductile SHCC.