Thermal and morphological studies of the segmented multiblock copolyesters containing 2,2,4,4-tetramethyl-1,3-cyclobutanediol and dimethyl-1,4-cyclohexane dicarboxylate were carried out using differential scanning calorimetry, small angle X-ray scattering, wide angle X-ray diffraction and dynamic mechanical analysis. Molecular origins of the thermal transitions appearing in copolyesters were assigned by the copolyester analysis at different temperatures. The hard segments in copolyesters underwent short-range and long-range ordering (crystallization) during cooling or annealing above glass transition temperature, as concluded from thermal and wide angle X-ray diffraction analysis. Annealing process affected the ordering in hard segments and annealing temperatures of 160 °C and above led to increased microphase mixing. The small angle X-ray scattering studies confirmed the microphase separated morphology of copolyesters and supported the argument of increased microphase mixing in copolyesters annealed at higher temperatures. The amount of sulfonate containing co-monomer and its presence in either hard or soft microphase affected the morphology of the copolyesters. Introduction of the sulfonate groups led to increased microphase mixing in copolyesters as well as destruction of long-range order in the hard segments.