In this work, permeable crystalline waterproof material was used as the research object, which was added into cement-based materials to fabricate cement-based permeable crystalline waterproof material (CCCW). X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) were applied to investigate the composition of CCCW. On this base, the effect of CCCW on mechanical properties to the samples were researched, and scanning electron microscope (SEM) as well as X-ray diffraction (XRD) were introduced to investigate micro-morphology and phase composition of the samples, which were combined with the relevant data about compress strength restoration ratio and permeability resistance to illuminate work mechanism of CCCW. It was confirmed that permeable crystalline waterproof material contained calcium oxide, sodium silicate, sodium disilicate, calcium carbonate, calcium hydroxide, PAH based water reducing agent and ethylenediaminetetraacetate. CCCW samples with permeable crystalline waterproof material loading exhibited excellent mechanical property, permeability resistance and self-healing property. The sample presented flexural strength at 7, 14 and 28 d of 2.65, 3.29 and 4.35 MPa, and exhibited compress strength of 12.11,14.57 and 16.77 MPa, respectively. The CCCW sample presented first permeability and second permeability of 0.8 and 0.9 MPa, which showed compress strength restoration at 7, 14, 28 and 56 d for 80.91%,90.35%, 100.44% and 105.90%, respectively. The work mechanism of CCCW has proposed: sodium silicate and sodium disilicate in permeable crystalline waterproof material reacted with Ca²⁺ in cement to form calcium silicate hydrate gel (C—S—H) and effectively repair the cracks. Calcium oxide, calcium hydroxide and calcium carbonate played as Ca²⁺ compensators and provided abundant free Ca²⁺, which could effectively promote the healing process of the cracks underwater environment. Calcium carbonate gradually dissolved in the water environment and produced Ca²⁺, CO₃^2- and HCO₃^-, the generated CO₃^2- and HCO₃^- could reacted with abundant Ca²⁺ to produce calcium carbonate crystal, which combined with C—S—H gel to blocked the crack structure of CCCW.