Cracks are inevitable in the use of cement-based materials. It takes a lot of resources to repair these cracks and prolong the service life of cement-based materials. Self-healing cement-based materials that can automatically repair cracks and improve the self-healing ability of cement-based materials have become the focus of current research. The current self-healing systems achieve impermeability recovery of matrix by the filling cracks. Few scholars have paid attention to the impermeability recovery through self-hydrophobic broken panels. In this paper, SEM, FTIR, core content titration, water flux test and contact angle test were carried out. The morphology, composition, core content and impermeability recovery effect of self-healing cement paste were prepared and characterized. Carbon nanotubes are used to improve the water resistance of isocyanate microcapsules, which possess a diameter of 237.6 ± 59.1 μm, distinct core-shell structure, and good dispersibility. The residual core fraction is 58.2 % after 21 days in Ca(OH)2 aqueous solutions. The microcapsules maintain integrity without breakage when mixed with fresh cement paste and have good bonding compatibility with cement matrix. When microcapsules are embedded into cement paste, the cracks could break the microcapsules releasing isocyanate to wet the broken panels. The isocyanates react with the moisture with the formation of polyurea, changing the contact angle of broken panels from near 0° to 118.4 ± 0.1°. The hydrophobic panels could retard the water penetration and recover the impermeability of cement paste. Based on this, a new self-healing mechanism of self-hydrophobic fracture surface to realize self-healing of impermeability of cement matrix is proposed.