The temperature-dependent deformation behavior of amorphous thin films of poly(1,4-cyclohexylenedimethylene terephthalate) (PCT), poly(ethylene terephthalate) (PET), and their copolymers was examined with variation of temperature and cyclohexylene linkage content by transmission electron microscopy. When subject to uniaxial tension, thin films of PET homopolymers and copolymers containing low content of cyclohexylene linkage showed a tendency of failure by crazing, whereas a transition from crazing to localized shear deformation occurred as the content of cyclohexylene linkage increased. When temperature was lowered to where secondary relaxation is suppressed, PCT and the copolymers showed transition of deformation mode from shear or mixed deformation to crazing, while no significant change was observed for PET. Whereas it has been considered that the change of deformation mechanism in thin films is governed by entanglement density, it was found that the transition in the deformation behavior obtained in PCT and the copolymers were highly correlated to the conformational transition of the cyclohexylene ring.