As the material performance and environment of marine concrete structures are random and time dependent, the perturbation stochastic finite element method（SFEM） for analysis of chloride ion diffusion in concrete, incorporating the time dependence into the mathematical model of chloride ion diffusion coefficient and surface chloride ion concentration was proposed. The Gaussian random field was used to model the chloride ion diffusion coefficient of concrete, while the local average method was employed to discretize the random field. According to the variational principle and the perturbation technique, the governing equations for the SFEM were presented, by which the mean value and covariance of chloride ion concentration could be determined. Comparing with test result and Monte Carlo finite element method（MCFEM）, the efficiency and accuracy of the presented method is demonstrated. It can be concluded that the random and time dependent chloride ion diffusion coefficient can significantly influence the process of chloride ion diffusion in concrete, while the effect of the time dependence of surface chloride ion concentration can be neglected for concrete structures exposed to chloride environment for a long term duration.