Time-resolved small-angle X-ray scattering (SAXS) analysis was performed on a series of poly(ethyleneco-1,4-cyclohexyldimethylene terephthalate)s (PECT copolymers) containing 1.6, 5.3, and 9.8 mol% 1,4-cyclohexyldimethylene (CHDM) units during isothermal crystallization and subsequent melting processes. The measured SAXS data were quantitatively analyzed to yield detailed information (scattering invariant quantity, Q; long period, L p ; lamellar crystal layer thickness, d c ; and amorphous layer thickness, d a ) about the crystal structure evolution and melting devolution behaviors. The Q value was found to be a very sensitive powerful probe for monitoring the crystallization and crystal melting processes. The structural evolution of the copolymers was dominated by the primary crystallization transition. The secondary crystallization effects contributed little to the structural evolution. The few secondary crystals present most likely formed fringed micelle structures that were very small and included a high degree of imperfections. The poor secondary crystal formation was attributed to the presence of bulky, kinked CHDM units, which introduced a high degree of steric hindrance. The high steric hindrance of the CHDM units resulted in their exclusion from the lamellar crystal layers and secondary crystals, and in their insertion into amorphous regions and layers. Overall, the CHDM comonomer units strongly perturbed the crystallization process and the morphological structure of the PECT copolymer. The effects of CHDM as a chemical modifier of poly(ethylene terephthalate)-based polymers may potentially be optimized in an effort to enhance the properties and processability of the polymer.