Our three-dimensional toroidal magnetohydrodynamics code [CLT (Ci-Liu-Ti, which means magnetohydrodynamics in Chinese)] is upgraded to CLTx in which the simulation domain extends to a scrape-off layer (SOL). Linear simulation results of resonant magnetic perturbation (RMP) for edge-localized-mode mitigation discharge 52340 in EAST Tokamak agree well with those from the MARS-F code. With the presence of the X-point and the SOL, the RMP amplitude and phase shift in the pedestal region, especially for a higher m mode, are largely affected by the resistivity in the SOL. A phase shift of π for resonant harmonics in vacuum and with a plasma response is observed, which is quite different from the π/2 shift due to the presence of screen current suggested in the previous studies. Simulation results with different resistivities suggest that the amplitude reduction and the phase shift of the resonant harmonics increase with decreasing the resistivity.