Nuclear graphite plays a crucial role in thermal-spectrum thorium molten salt reactors (TMSRs) as both the neutron moderator and the construct for the coolant flowing channel. When subjected to irradiation and elevated temperatures, graphite components experience considerable deformation due to a combination of dimensional changes, thermal expansion, irradiation creep, elastic deformation, and changes in thermomechanical characteristics. The lifespan of the graphite component is a limiting factor in TMSR designs as it strongly correlates with the dimensional changes of the graphite. To evaluate the thermal and mechanical reactions of graphite component under TMSR core conditions, it is necessary to couple models of thermal-hydraulics, neutronics, and thermal-mechanics. This paper presents an enhanced methodology for analyzing the deformation of graphite components using the finite element method. Then, this method was applied to analyze a 10-year deformation history of a hexagonal prism assembly (HPA) and it was compared with the traditional hexagonal round channel assembly (RCA). The results demonstrate that the stress–strain field of both types of graphite components undergo significant variations with the increasing neutron fluence from irradiation. HPA graphite exhibits a slower deformation as compared to RCA graphite when subjected to identical operating conditions. In this case, HPA graphite has a lifespan of approximately 10 years, while RCA graphite lasts only 8.8 years.