Concrete is a multiphase composite material composed of coarse aggregate, cement mortar, and interface transition zone (ITZ). It is of great significance to study the effect of ITZ and coarse aggregate on chloride microscopic diffusion behavior for predicting the service life of reinforced concrete (RC) structures. By introducing the random distribution function, a random coarse aggregate model considering the randomness of the thickness of the ITZ was established. Furthermore, a two-dimensional (2D) chloride ion diffusion mesoscopic model was developed by specifying different diffusion properties for different phase materials of concrete. Moreover, the effects of coarse aggregate rate, ITZ thickness, and ITZ diffusion property on chloride ion diffusion behavior were investigated in this paper. The research showed that the aggregate has hindrance and agglomeration action on chloride ion diffusion. Although the volume content of the ITZ was very small, less than 0.2% of the total volume of concrete, the effect of the ITZ on the chloride diffusion in concrete cannot be ignored. More importantly, the mechanism of promoting chloride diffusion in the ITZ was revealed through the chloride diffusion trajectory. The research revealed the transmission mechanism of chloride ions in the meso-structure of concrete and provides theoretical support for the design of RC structures in coastal areas.