The integrated modular avionics (IMA) system has coupled cross-linked support characteristics between physical resource entities and logical functions, and the existing resource allocation methods, which mainly consider system performance and resource utilization, do not consider the associated impact of fault propagation among resource entities. Aiming at the fault propagation risk in the resource allocation process of the IMA system, a hierarchical model of the IMA system is established. The fault propagation behavior caused by coupling association during the physical realization of the function layer logical architecture is analyzed, and the impact of different resource allocation methods on the fault propagation behavior is determined. Secondly, resource capacity constraints are established according to the resource requirement for hosted function, and the fault propagation risk model of the IMA system is constructed by considering the fault propagation impact factor, the relative importance of nodes, and the function safety criticality. The resource allocation method is evaluated according to the fault propagation risk model, and a heuristic algorithm is applied to optimize the resource allocation method of the IMA system. The simulation results show that the average propagation probability of the optimized resource allocation scheme decreases by 17.4%, and the overall fault propagation risk of the resource network decreases by 50.3%, indicating that the proposed resource allocation method can effectively improve the safety of the IMA system.