The reinforcement in concrete alters the pathway for chloride transporting and in turn causes the chloride concentration to accumulate faster near the reinforcement closest to the exposed surface. A mass conservation matrix equation under the non-stable diffusion based on the Fick’s second law was derived. Hereby, a numerical simulation method for predicting chloride concentration in concrete was established utilizing the compiled module based on FEA. The validity of the method was verified by the comparison with the analytical results. The proposed method has a wider applicability for predicting the service life of RC structures. And it can be applied flexibly to any complicated section shape of RC members with multi-boundary attacked by chloride and the reinforcement considered simultaneously.