Abstract The flanges of 10 MW high temperature gas-cooled reactor (HTR-10) pressure vessel play an important role in sealing the primary coolant of Helium. They are bolt-connected with a metallic O-ring and a welded Ω-ring. An elastic–plastic nonlinear analysis was performed to evaluate the stress and deformation of the contact flanges with the finite element software of MSC MARC 2000. The multi-step loading process was employed to simulate the processes of pre-tightening and pressurizing of the HTR-10 pressure vessel. The structural effects of the flanges on the opening and the shifting of the HTR-10 pressure vessel flanges at the O-ring position were studied to determine the flange height and the head closure thickness. The good sealing performance of the O-ring and the Ω-ring was verified both numerically and experimentally. The finite element model analysis results compared well with the hydraulic test of the HTR-10 pressure vessel. The results show that the flanges can meet the strength requirement and that the O-ring and the Ω-ring can effectively seal the HTR-10 pressure vessel during both pre-tightening and pressurizing.