The pulling core rivet is widely used in the field of aviation manufacturing and assembly. There is a quantitative standard for the protrusion of the core rod section relative to the surface of the nail sleeve head (flatness of core rod), but the influence of flatness of core rod on the mechanical properties of the connected structure is not clear. In order to solve this problem, the static and fatigue performance tests of the assembly structure induced by the flatness of the core rod were carried out. The assembly and static performance of the structure are simulated and verified. Through experimental research, it is found that the average shear failure strength of samples with qualified core rod flatness is 9570.535 N, and the standard deviation is 107.001 N; the average shear failure strength of samples with unqualified core rod flatness is 9532.14 N, and the standard deviation is 327.261 N. Compared with out-of-tolerance samples, the standard deviation of qualified samples is more stable. In the fatigue test, the average number of fatigue cycles of qualified core rod evenness samples is 456770, and the average number of fatigue cycles of unqualified core rod evenness samples is 456022.7, so the fatigue strength is less affected by this aspect. The simulation of riveting shows that there is almost no difference in the absolute interference of the core rod under the two conditions. This conclusion explains why there is not much difference in the shear force between the two groups of tests, and it is found that there is almost no difference in the force-displacement curves between the two groups during the simulation process, which further verifies the test conclusion.