Flow instability is investigated in a two-dimensional channel with thin baffles placed symmetrically in the vertical direction and periodically in the streamwise dircetion. At low Reynolds numbers, the flow is steady and symmetric. Above a critical Reynolds number, the steady flow undergoes a Hopf bifurcation leading to unsteady periodic flow. As Reynolds number further increases, we observe the onset of secondary instability. At high Reynolds numbers, the two-dimensional periodic flow becomes three dimmensional. To identify the onset of secondary instability, we carry out Floquet stability analysis. We obseved the transition to 3D flow at a Reynolds number of about 125. Also, we computed dominant spanwise wavenumbers near the critical Reynolds number, and visualized vortical structures associated with the most unstable spanwise wave.