Hydrophobic modification of cement-based coating is beneficial to improving its protective effect, but it leads to poor dispersion of coating, weakening of physical properties and durability of coating. In this paper, a highly stable/hydrophobic modified polyacrylate emulsion was prepared by using hydroxy-containing polydimethylsiloxane (PDMS) as a second oil phase, and a high durability polymer cement-based protective coating was further constructed. The modified emulsions with good stability and hydrophobicity can be obtained by matching the molecular weight and dosage of PDMS and emulsifying the shear rate. Little stratification occurs after 30 d, the contact angle of latex film is increased by 24.9%, and the water absorption is decreased by 28.94%. The prepared polymer cement-based coating has superior mechanical properties, hydrophobicity, UV aging resistance, seawater and alkali immersion resistance, and the chloride ion permeability coefficient is only 0.193×10-6 mm2/s. In addition, the modification mechanism of emulsion and the durability enhancement mechanism of coating were also analyzed.