[Purposes] This paper aims to study the effects of nano-silica (NS) and siloxane on the superhydrophobic modifications and properties of cement-based materials. [Methods] The best ratios of modified materials, including dodecyltrimethoxysilane (DTES), NS, and polycarboxylate superplasticizer (PCE) for cement-based materials, were selected by the orthogonal test method. The strength tests, the heat of hydration tests, the contact angle measurements, and the capillary water absorption tests were conducted to evaluate the effects of the modified materials on the mechanical and hydrophobic properties of the cement. [Findings] The best mass mixing ratios of DTES, NS, and PCE are 3.00%, 1.80%, and 0.25%, respectively. The water contact angle on the surface of the modified cement specimen is up to 152.50°. The capillary water absorption coefficient is reduced by more than 91%, and the flexural strength after 3 d and the compressive strength after 28 d are reduced by 19% and 12%, respectively. [Conclusions] The combined effect of the modified materials results on the surface of cement-based materials is superhydrophobic and of excellent resistance to water penetrations. The strength of cement is affected by DTES, while the compressive strength and the later flexural strength are enhanced by NS.