The integral analysis of reactor cooling system (RCS) and containment is becoming increasingly important for advanced reactors, especially reactors with passive safety technology. In this study, a new three-dimensional containment thermal–hydraulic analysis method is established using the equations and solutions similar to the reactor cooling system program for a strong coupling calculation of the containment and RCS. The integral program was verified by simulating the gravity drain line break accident of the PUMA test facility. The simulation results indicate that the coupled RCS-containment integral analysis program can be applied for analyzing the thermal–hydraulic coupling of the containment and RCS. The integral program was applied to simulate the LOCA for the RCS-containment integral system of AP1000. The results indicate that the integral program can be applied to analyse the AP1000 LOCA.