Cement-based materials are non-uniform porous materials that are easily permeated by harmful substances, thereby deteriorating their structural durability. In this work, three ionic paraffin emulsions (IPEs) (i.e., anionic paraffin emulsion (APE), cationic paraffin emulsion (CPE), and non-ionic paraffin emulsion (NPE), respectively) were prepared. The effects of incorporation of IPEs into cement-based materials on hydrophobicity improvement were investigated by environmental scanning electron microscopy (ESEM), Fourier transform infrared (FTIR) spectroscopy, transmission and reflection polarizing microscope (TRPM) tests and correlation analyses, as well as by compressive strength, impermeability, and apparent contact angle tests. Finally, the optimal type and the recommended dose of IPEs were suggested. Results reveal that the impermeability pressure and apparent contact angle value of cement-based materials incorporated with IPEs are significantly higher than those of the control group. Thus, the hydrophobicity of cement-based materials is significantly improved. However, IPEs adversely affect the compressive strength of cement-based materials. The apparent contact angle mainly affects impermeability. These three IPEs impart hydrophobicity to cement-based materials. In addition, the optimal NPE dose can significantly improve the hydrophobicity of cement-based materials.