Modern aircraft tend to use fuel thermal management systems to cool onboard heat sources. However, the design of heat transfer architectures for fuel thermal management systems relies on the experience of the engineers and lacks theoretical guidance. This paper proposes a concise graph representation method based on graph theory for fuel thermal management systems, which can represent all possible connections between subsystems. A generalized optimization algorithm is proposed for fuel thermal management system architecture to minimize the heat sink. This algorithm can autonomously arrange subsystems with heat production differences and efficiently utilize the architecture of the fuel heat sink. At the same time, two evaluation indices are proposed from the perspective of subsystems. These indices intuitively and clearly show that the reason for the high efficiency of heat sink utilization is the balanced and moderate cooling of each subsystem and verify the rationality of the architecture optimization method. A set of simulations are also conducted, which demonstrate that the fuel tank temperature has no effect on the performance of the architecture. This paper provides a reference for the architectural design of aircraft fuel thermal management systems. The metrics used in this paper can also be utilized to evaluate the existing architecture.