Numerical simulation is carried out to investigate the effect of the boundary condition of two lateral end-plate walls on the flow structure in the wake of a flow crossing a yawed circular cylinder. Two typical boundary conditions, nonslip and periodic, are investigated. It is revealed that the boundary condition of the two end-plates has a significant effect on the flow behaviors in the wake. Under the nonslip boundary condition, the vortex structure in the wake exhibits a tapering shape to the tip end. The flow pattern is formed in the wake as the streamlines on the tip side are becoming denser while the streamlines on the base end are becoming sparser. Spectral power analysis of the local lift coefficient shows that the frequency distribution exhibits axial variation. On the base side, the frequency distribution is broadband. On the tip side, there are two peak frequencies: the larger one corresponds to the value predicted by the independence principle, and the smaller one is generated by the secondary axial flow separation from the rear cylinder wall. Under the periodic condition, the numerical results show that organized Strouhal vortex is shed in the wake in the same way as to the flow orthogonally passing a cylinder and the independence principle is still applicable.