A series of novel poly(trimethylene terephthalate-co-1,4-cyclohexylene dimethylene terephthalate) (PTCT) with various compositions were synthesized by melt polycondensation of 1,3-propanediol, 1,4-cyclohexanedimethanol and dimethyl terephthalate. The resulting copolyesters were characterized using 13C and 1H nuclear magnetic resonance. The average length of both trimethylene terephthalate (TT) and cyclohexylene dimethylene terephthalate (CT) sequences varies from 1 to 10, and the chain structure is statistically random. The crystallization was investigated using wide angle X-ray diffractometer (WAXD) and differential scanning calorimeter. The WAXD patterns can be divided in two groups according to the composition: copolyesters with less than 35 mol% CT content exhibit PTT-type lattice, and those with CT unit content higher than 42 mol% crystallize with the PCT-type lattice. The crystallizability of CT sequence is higher than that of TT sequence. Thermodynamic analysis shows that the comonomer is excluded from the PTT-type or PCT-type crystal of the copolyesters. The thermal decomposition temperature of copolyesters increases with increasing CT content, and their thermal stability is improved as compared to that of PTT.