To prevent primary water stress corrosion cracking (PWSCC), water jet peening (WJP) has been used on the welds of Ni-based alloys in pressurized water reactors (PWRs). Before WJP, the welds are machined and buffed in order to conduct a penetrant test (PT) to verify the weld qualities to access, and microstructure evolution takes place in the target area due to the severe plastic deformation. The compressive residual stresses induced by WJP might be unstable under elevated temperatures because of the high dislocation density in the compressive stress layer. Therefore, the stability of the compressive residual stresses caused by WJP was investigated during long-term operation by considering the microstructure evolution due to the working processes. The following conclusions were made: The compressive residual stresses were slightly relaxed in the surface layers of the thermally aged specimens. There were no differences in the magnitude of the relaxation based on temperature or time. The compressive residual stresses induced by WJP were confirmed to remain stable under elevated temperatures. The stress relaxation at the surface followed the Johnson-Mehl equation, which states that stress relaxation can occur due to the recovery of severe plastic strain, since the estimated activation energy agrees very well with the self-diffusion energy for Ni. By utilizing the additivity rule, it was indicated that stress relaxation due to recovery is completed during the startup process. It was proposed that the long-term stability of WJP under elevated temperatures must be assessed based on compressive stresses with respect to the yield stress. Thermal elastic-plastic creep analysis was performed to predict the effect of creep strain. After 100 yr of simulated continuous operation at 80% capacity, there was little change in the WJP compressive stresses under an actual operating temperature of 623 K. Therefore, the long-term stability of WJP during actual operation was analytically predicted.