This study conducts a numerical simulation investigation on the flow field characteristics and fluid-elastic instability of the spatially bent tube structure in the intermediate heat exchanger (IHX) of a fast reactor. The inherent frequencies of the unique structure of the IHX spatially bent tube are calculated by using the wet modal method. They are employing Computational Fluid Dynamics (CFD) in conjunction with a fluid-structure coupling model, establishing an elastic tube model. Considering the bundle concentric circles arrangement, the “transition” arrangement is selected as the model to simulate the fluid-elastic instability. By the analysis of critical flow velocity, displacement, and the main vibration direction, the results indicate that the fluid-elastic instability of the tube bundle with a transition arrangement is mainly manifested by more severe vibrations in the bent tube segment. The instability flow velocity in the straight tube segment, ranging from 4.64 to 4.84 m/s, is greater than the instability flow velocity of 2.85 m/s in the bent tube segment. This study provides theoretical support for the design and operation of the intermediate heat exchanger in fast reactors, offering references for considering tube bundle arrangement and fluid-elastic instability in engineering practice.