Secondary instability in an obstructed channel is investigated using direct numerical simulation. Flow geometry under consideration is a plane channel with two-dimensional thin obstacles mounted symmetrically in the vertical direction and periodically in the streamwise direction. Flow separation occurs at the tip of the sharp obstacles. As a basic flow, we consider an unsteady periodic solution which results from Hopf bifurcation. Depending on the Reynolds number, the basic flow becomes unstable to three-dimensional disturbances, which results in a chaotic flow. Numerical results obtained are consistent with experimental findings currently available.