Integrated modular avionics architecture has become the most attractive idea to enhance system capability as well as improve efficiency. However, this architecture makes designing a system configuration scheme difficult because multiple resources are shared to support different functions that may have been irrelevant before. This article introduces a method to optimize the configuration scheme for an integrated modular avionics system while considering functional redundancy requirements. Not only the allocation scheme, which illustrates the relationships between functions and shared resources is taken into account, but also the resource scheme, which illustrates how many shared resources are enough to cover the functional requirements is considered as a part of the configuration scheme. Toward a generic integrated modular avionics system with functional redundancy requirements, we first give a configuration scheme model as well as its related schedulability and reliability constraints. Then, the optimization process of the configuration scheme is formalized as a combination of a constraint satisfaction problem and a constraint optimization problem. Specifically, it is decomposed into two steps including: 1) finding a resource scheme which has the lowest cost but still satisfies the constraints based on a forward checking algorithm; 2) finding its corresponding allocation scheme which distributes the targeted functions to different resources as evenly and low-coupled as possible based on the NSGA-II algorithm. Finally, an example is used to prove the effectiveness of the method. The optimization method can serve as a guide to design a configuration scheme for the integrated modular avionics system.