The ingress of chloride ions in concrete induces the corrosion of reinforcement, leading to a degradation of the mechanical performance of the intended structural applications. The incorporation of crystallizing admixtures imparts autogenous healing to conventional concrete, enabling cracks to seal by themselves and thereby reducing the infiltration of chloride ions. Recognizing the inherent heterogeneity of plain concrete, this study formulates a mesoscopic numerical model in the framework of finite element method. The model conceptualizes concrete as a three component structure: coarse aggregate, mortar matrix, and interfacial transition zones (ITZs). To account for the influence of the self-healing phenomenon in concrete, two further phases representing cracks and damage zones (DZs) are introduced. The coarse aggregate phase is considered impermeable, with chloride ion diffusion assumed to occur in the remaining four phases. The self-healing process of cracks was simulated by using the moving mesh technique in COMSOL, with reference to the method of establishing the kinetic law of crack self-healing in the follow-up of Horizon 2020 ReSHEALience project, undertaken in the project MUSA, funded through the Italian National Resilience and Recover plan. Validated against experimental data, the model not only reproduces the crack closure process but also offers predictions on chloride transport. This simulation model contributes to the exploration of concrete resistance to chloride permeability, elucidates the transport mechanism of chloride ions within self-healing concrete, and provides insights for designing durable concrete structures to mitigate the corrosion of steel reinforcement or steel fibers.