The Ti600/TC18 dissimilar titanium alloy joints were prepared by inertia friction welding (IFW). Then, stress-relief annealing and two-stage annealing were performed to optimize the microstructure and properties of the original joints, the purpose of them is to improve the structure and performance of the joints. Then, the microstructure, phase composition, tensile properties, microhardness, and fracture morphology of the joints after heat treatments were investigated. The results showed that after stress-relief annealing, the microstructure of the joints was almost similar to that of the specimen before annealing; the weld zone (WZ) of the joints was composed of fine recrystallized grains and α′, and the more β phases underwent a martensitic transformation. The shapes and sizes of αp phases were increased after two-stage annealing; its percentage content was decreased. The tensile properties and the microhardness values of the joints undergoing stress-relief annealing were relatively higher than that of the joints undergoing two-stage annealing; there was no obvious change in the plasticity of the joints. It was confirmed that the stress-relief annealing microstructure was composed of α′ and β phases, which were beneficial to the properties of the joints. However, the αs phases were coarsened after two-stage annealing, and the properties of the joints were reduced.