In marine environment, chloride ions intrusion into marine reinforced concrete (RC) structure (MRCS) and hence induced the corrosion of steel reinforcements is a relatively long-term process. It is costly to carry out the long-term experimental studies on natural intrusion of chloride ions into concrete; hence, the high-efficiently numerical simulation method is used for exploring the chloride ions transport into MRCSs. Previous studies have generalized the concrete composites in MRCSs as a transport medium of homogeneous and isotropic, and the macro-scopic model was applied to analyse the chloride ion transport behaviour of RC. However, RC is a typical heterogeneous and multi-phase composite, and these phases, especially the steel reinforcement phase, included in RC can obviously impact the chloride ions transport laws. Using the generalized macro-scopic numerical model of RC cannot be consistent with the actual conditions. For this study's exploration, the meso-scopic structure of RC is composed of the mortar, coarse aggregate, steel bar, and interfacial transition zone (ITZ), and a 3D meso-scopic model of RC composites is established based on the random generation and random placement algorithm of 3D spherical coarse aggregate. Particularly, the influence of steel reinforcement presence on aggregate distribution in a certain area around the rebar embedded in the RC meso-scopic model is considered and simulated. Based on the finite element method (FEM) of dilute substance transfer, the numerical simulation analysis of chloride ions transport into RC 3D meso-scopic model is conducted, and the transport features of chloride ions into RC meso-scopic model as well as the chloride concentration variation rules in front of the rebar are explored. The precision of numerical simulation method and its computational results for determining the chloride ions transport into RC meso-scopic model are validated in accordance with the experimental measurements. The findings of this paper's studies can greatly promote the development of the basic theory for RC structural durability, which have important scientific significance.