In order to investigate the effect of shim compensation for nonuniform gaps in aircraft assembly, the influence of the shims with different material and parameters on bolted joints is studied in this paper. According to the real material and assembly conditions of the aircraft joint structures, the specimen and experiment are designed to obtain the tensile performance of the joint structures with different shims. A three-dimensional finite element model, which incorporates the Johnson–Cook material property of the alloys, traction-separation law of liquid shims, contact relationships between the joint elements, and boundary conditions of the tensile process, is established with the specimen configurations. After validating through comparing with the experimental results, the modeling method is adopted to simulate the tensile response of the bolted joints with shims. Furthermore, both the influence of the shim material and thickness on the mechanical behaviors of bolted joints is investigated in detail. Shims can considerably reduce the assembly stress of joint structures and improve the joint stiffness and load capacity, and this effect is more remarkable with the increase of gap values. Liquid shims improve the joint stiffness due to its cohesive ability, while solid shims improve the joint load capacity. Hybrid shims possess a composite shimming effect of liquid and solid shims. Whatever the shim material is applied, the joint stiffness and strength drop with the growth of shim thickness, so strict deviation control method should be taken to ensure the assembly gaps as small as possible. The research results enhance the knowledge of shimming effect on joint structures, and thus offer positive guidance for practical application in aircraft assembly.