Marine concrete has been subjected to the dual threats from cracking and the corrosion of ion. To achieve the self-healing of cracks in concrete and the binding of Cl− and SO42− in marine environment, a novel compound mineral capsule with MgO expansive agent, quicklime and metakaolin as healing agents was developed in this study. To evaluate the ion binding capacity of capsules, after the broken capsules were immersed in synthetic seawater for different times, the concentrations of Cl− and SO42− in seawater were measured, and the binding products on the capsules were analyzed. Then the capsules were incorporated into mortar in varying amounts, and the self-healing capacity at different healing ages was quantitatively characterized by the tests of crack observation, sorptivity and water permeability. Through microstructure analysis of healing products, the self-healing process and mechanism of the mortar containing capsules under marine environment were revealed. Results showed that the compound mineral capsules effectively bound Cl− and SO42− by forming Friedel's salt and ettringite. The addition of capsules significantly improved the crack closure and conspicuously reduced the transport performance of cracked mortar. With the dosage of capsules increased, the self-healing process was accelerated. The underlying reasons were that the capsules promoted the formation of Friedel's salt, ettringite, hydrotalcite and brucite, in addition to portlandite, calcite and C-S-H. Under the filling effect of these products, cracks achieved self-healing while Cl− and SO42− were simultaneously bound. Consequently, the impermeability of the cracked cementitious materials in marine environments was effectively increased.