To study the non-uniform corrosion of steel rebar induced by chloride ions invasion under marine environment, the three-dimensional characteristic distribution of aggregates and pores in concrete was numerically extracted and reconstructed through X-ray CT technique. Based on the 3D in-situ meso-structure model of concrete, the random characteristics of chloride ions transport in concrete was investigated by numerical simulation. Through a fitting and hypothesis test on the concentration distribution histogram of chloride ions, a reliable probability density distribution function of chloride ions concentration was proposed. And the influence of ITZ and aggregate shape on the random diffusion of chloride ions was studied. The research indicates that that the spatial distribution of coarse aggregates and pores is the main reason leading to the non-uniform distribution of chloride ions. The chloride ions concentration under a certain time follows the Lognormal distribution. The discreteness of chloride ions distribution in concrete decreases when the interfacial transition zone is not considered in the model. And an increase of the irregularity of aggregate shape will cause an increase in the tortuosity of chloride ions transport path, and the discreteness of chloride ions distribution will enhance accordingly.