To provide a high-performance marine engineering material, the microstructure and impermeability of calcium aluminate cement (CAC) containing metakaolin (MK) were studied. The chloride penetration resistance of the CAC-MK and Portland cement (PC) mortars was assessed based on physical and chemical barrier effects. The results show that the alumina in MK is more easily dissolved than silica, which inhibits the transformation of CAH10 and prevents microstructural deterioration. Adding 7.5% and 15.0% MK reduces the volume of large pores in the 3-day-old CAC paste by 49.8% and 69.1% while increasing the volume of pores smaller than 50 nm by 175.6% and 242.5%, respectively. Moreover, the microstructure of MK-containing CAC pastes becomes denser with age when cured at 40 °C, enhancing the mechanical strength and water penetration resistance. The CAC mortar containing MK exhibits better resistance to chloride attack than PC mortar, due to the stronger chloride binding capacity and migration resistance.