Cement-based materials are highly hydrophilic, and aggressive substances in service environment often penetrate into the cement-based materials through the transmission of water, resulting in corrosion of steel bars, carbonization of concrete, and other hazards. In this paper, two types of microbe cells were applied to improve the hydrophobic properties of the mortar specimens. The results show that the contact angle of the mortar specimens increases to 122.7° and 112.1° after the addition of Starmerella bombicola CCRC22302 and Bacillus sphaericus LMG22257, respectively. The diffusion rate and absorption rate of water on the fracture surface are obviously slowed down. The capillary water absorption is decreased by 39% in the groups added with 2.5% (in mass) Starmerella bombicola by mass of cement. The bacterial cell improves the hydrophobicity through the combined action of the rough structure and its hydrophobicity. However, it is indicated that the flexural and compressive strengths of the mortar specimens are significantly decreased, thus becoming a challenge for the practical application.