Flexible copper clad laminate has been used to fabricate flexible electronics such as bio-inspired tactile sensor, microfluidicsbased sensor, and flexible printed circuits board. Herein, the effects of thermal property difference between the component layers on the residual interfacial deformation in a flexible copper clad laminate occurring during roll-to-roll composite film manufacturing were analyzed. The thermal behaviors of polyimide film and copper meshes in the laminate were examined, and it was found that differences of the coefficient of thermal expansion and elastic modulus between the two components could cause the residual deformation in the laminate. The three factors affecting the residual strain due to the thermal characteristic difference, i.e., temperature and pressure of the lamination roll and web tension, were selected in the controllable operating conditions in a roll-to-roll lamination process. Mathematical models to estimate the elastic and thermal residual strains according to the factors were developed and experimentally verified. Finally, the effects of the three factors on the residual strain in the laminate were determined using the developed model. In this study, we demonstrate that, in the lamination process, the thermal strain of the laminate component materials after thermal cycling generates a significant residual deformation, which causes defects in the flexible copper clad laminate. The developed model can be used to accurately estimate the residual elastic and thermal residual strains occurring during the roll-to-roll manufacturing according to the process conditions.