A series of novel polyesters containing conjugated diacetylenes (DA-polyesters) were prepared from various diacetylene diols with/without methyl side groups and isomers of aromatic acid chlorides via an interfacial condensation. A fully aliphatic DA-polyester was also prepared for comparison. All synthesised DA-polyesters are soluble in m-cresol, and the intrinsic viscosities were measured. In addition, compact and coherent films and sheets can be obtained from some of the polymers via solution or melt casting. The structure, morphology, and properties were characterized using spectroscopic methods, including FTIR, Raman, and WAXD and thermal analysis including TGA, DSC techniques. DMA was carried out on the solution-cast thin films and melt-processed samples. Close correlation was found between the structure and properties in these DA-polyesters. In particular, through analysis using isothermal DSC and Raman spectroscopy, the solid-state reactivity of the diacetylene groups in these polyesters was found related to the interchain spacings, which are, in turn, controlled by the molecular structure of the polymers. Results have shown that the aliphatic DA-polyester behaves very differently compared to the aromatic ones. Distinct differences were also observed among meta- and para-disubstituted isomers of the DA-polyesters. Furthermore, the introduction of methyl side groups has dramatically affected the thermal and thermal mechanical behavior by altering the interchain spacing of the polymers.