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We fabricated flexible spin valves on polyvinylidene fluoride (PVDF) membranes and investigated the influence of thermal deformation of substrates on the giant magnetoresistance (GMR) behaviors. The large magnetostrictive Fe81Ga19 (FeGa) alloy and the low magnetostrictive Fe19Ni81 (FeNi) alloy were selected as the free and pinned ferromagnetic layers. In addition, the exchange bias (EB) of the pinned layer was set along the different thermal deformation axesα31 orα32 of PVDF. The GMR ratio of the reference spin valves grown on Si intrinsically increases with lowering temperature due to an enhancement of spontaneous magnetization. For flexible spin valves, when decreasing temperature, the anisotropic thermal deformation of PVDF produces a uniaxial anisotropy along theα32 direction, which changes the distribution of magnetic domains. As a result, the GMR ratio at low temperature for spin valves with EBkα32 becomes close to that on Si, but for spin valves with EBkα31 is far away from that on Si. This thermal effect on GMR behaviors is more significant when using magnetostrictive FeGa as the free layer.