A fourth-order compact finite difference scheme was developed to solve the model equation of simulated moving bed, which has a boundary condition that is updated along the calculation process and cannot be described as an explicit function of time. Two different methods, direct method and pseudo grid point method, were proposed to deal with the boundary condition. The high accuracy of the two methods was confirmed by a case study of solving an advection-diffusion equation with exact solution. The developed compact finite difference scheme was then used to simulate the SMB processes for glucose-fructose separation and enantioseparation of 1,1'-bi-2-naphtol. It was found that the simulated results fit well with the experimental data. Furthermore, the developed method was further combined with the continuous prediction method to shorten the computational time and the results showed that, the computational time can be saved about 45%.