Based on the improved genetic algorithm and 8 neighborhood boundary tracking method, this paper adopts the real concrete section digital image to obtain binary image and extract the boundary coordinates of coarse aggregate. According to the extracted coordinates, a program was directly compiled to generate ITZ, and the real concrete mesoscopic model was obtained. Then, the obtained concrete mesoscopic model was imported into COMSOL software to simulate the process of chloride ions transporting the concrete in the underwater area of the ocean, and the cloud chart of chloride ions concentration in the concrete at different time was obtained. The results show that the modeling and simulation methods used in this paper are consistent with the experimental results of long-term exposed concrete in sea, which can be used to study and evaluate the durability of concrete under marine environment. The presence of the ITZ will accelerate the diffusion of chloride ions into the concrete. The greater the thickness is, the faster the diffusion process will be. The thickness of the interface area will double, and the apparent chloride ion diffusion coefficient of concrete will increase by 12.3%. By comparing the chloride ion transport simulation results of the real concrete mesoscopic model and the circular random aggregate model generated by parametric generation, it is found that the concentration of chloride ions in the circular random aggregate model is always smaller than that in the real microscopic model.