Based on welding heat transfer theory, heat elastoplasticity theory and phase transformation theory, welding residual stress in multi-layer welded joint of 9% Ni steel for liquefied natural gas (LNG) storage tanks was simulated using SYSWELD finite element analysis software. Taking into account nonlinear relationships between temperature and mechanical properties, together with influence of transformation latent heat on temperature field, double ellipsoid heat source model was applied in the simulation of the three fields (temperature field, microstructure field and stress-strain field). Distribution pattern of welding residual stress in 9%Ni steel welded joint was obtained through numerical simulation. Results showed that heat affected zone (HAZ) showing high-level residual stress was the main stress concentrated part of the welded joint. Longitudinal residual stress appeared to be tensile in the weld and HAZ, and compressive in regions remote from the weld. A match of low heat input and high interpass temperature should be employed to lower residual stress level in HAZ. Simulation results were well consistent with theoretical analysis.