In self-healing cement-based materials, the interface between microcapsules and cement matrix determines the probability of microcapsules triggered by cracks, which affects the self-healing effect. Aiming at the interface bonding problem of water absorbent microcapsules, the surface of epoxy/calcium alginate microcapsules was modified with silane coupling agent KH550 to improve the interface bonding between calcium alginate microcapsules and cement matrix. The X-ray photoelectron spectrometer and inductively coupled plasma emission spectrometer were used to characterize the bonding condition of silane coupling agent on the surface of microcapsules. The pore structure of cement-based materials was analyzed by mercury injection method, and the impermeability and self-healing effect of cement-based materials were tested. The results show that the silane coupling agent forms the chemical bonding with the calcium alginate on the outer wall of the microcapsule. The interface between the microcapsules and the cement matrix is effectively improved. The number of harmful pores in the cement matrix is reduced, and the number of harmless and less harmful pores increases. The impermeability and self-healing effect of cement-based materials are improved.