For concrete structures in offshore areas, chloride ion erosion is one of the main factors affecting durability. It is crucial to evaluate the chloride ion permeability resistance of concrete structures. In this paper, a finite element simulation of the chloride ion diffusion process in concrete is conducted. A mass diffusion finite element model based on a random aggregate approach is established to investigate the influences of an aggregate, the interface transition zone, and micro-cracks on the chloride ion diffusion coefficients in concrete. The results show that the mass diffusion finite element analysis based on the exponential function model and the power function model can effectively simulate the chloride ion diffusion process in concrete. In addition, the data reveal that volume fraction and distribution aggregates considerably affect chloride ion diffusivity in concrete. Also, the interface transition zone significantly accelerates chloride ion diffusion in concrete. Moreover, this acceleration effect exceeds the barrier effect of an aggregate.