In this paper, the flexural strength, compressive strength, water absorption and unsteady chloride ion migration coefficient were used to investigate the effect of styrene-butadiene rubber powder (SBR)/nano SiO2 (NS) on strength and impermeability of cement-based materials. The hydration products and microstructure of cement-based materials were analyzed by XRD, DSC-TG, FTIR, SEM-EDS and MIP. Results show that complex SBR/NS significantly improves the early strength degradation of cement-based materials caused by single SBR. Both single SBR and complex SBR/NS reduce the water absorption, water absorption rate and unsteady chloride ion migration coefficient, and the effect of complex SBR/NS is better than that of single SBR. The microscopic test shows that the single SBR reduces the content of Ca(OH)2 and the number of harmful pores and more-harmful pores and increases the integrity of the structure. The complex SBR/NS further reduces the content of Ca(OH)2, promotes the hydration reaction to generate more C-S-H, improves the polymerization degree of C-S-H, decreases the most probable aperture, reduces the amount of less-harmful pores, harmful pores and more-harmful pores, lowers the Ca/Si ratio of hydration products, and thus enhances the flexural strength, and compressive strength and improves the impermeability of the sample.