Photoinduced orientational behavior of a polymethacrylate (CN6) and a polyester (p6a12) with p-cyanoazobenzene side chains was studied to reveal the structural effect of the liquid crystalline polymer backbones. Irradiation with linearly polarized W light resulted in the reorientation of the azobenzene for both polymers toward the direction perpendicular to the electric vector of the incident light. The induced orientation can be slowly amplified by thermal Z-to-E isomerization and be facilitated by irradiation with visible light. For p6a12 with the long alkylene and carbonyl groups in main-chain cooperative orientation of main chains with p-cyanoazobenzene side chains was confirmed using FT-IR spectroscopy, contrary to the case of CN6. Furthermore, in-situ observation of changes in photoinduced birefringence by ellipsometry revealed that thermal treatment plays a significant role in levels of molecular orientation in polymer matrices.