Three series of even-odd aliphatic copolyesters, poly(hexamethylene gluarate-co-hexamethylene pimelate) (PHGP), poly(hexamethylene pimelate-co-hexamethylene azelate) (PHPA), and poly(hexamethylene gluarate-co-hexamethylene azelate) (PHGA), were firstly synthesized derived from even diol of 1,6-hexanediol with odd diacids of glutaric acid, pimelic acid or azelaic acid, respectively. Then, their cocrystallization behaviors were systematically investigated by DSC, WAXD, and POM techniques. It is found that both PHGP and PHPA showed isodimorphism with a characteristic eutectic behavior observed from the plot of melting point versus composition, however, PHGA exhibited strict isomorphism in the whole composition range without a eutectic point. WAXD studies also confirmed the unique isodimorphism and isomorphism behaviors for even-odd copolyesters. The only slight change of the methylene number in alkyl unit of comonomers could generate so large difference in crystallization behavior, which exhibits unique physicochemical properties and structure-properties correlations in such even-odd copolyesters. Furthermore, the difference in cocrystallization miscibility effect of comonomers was analyzed by thermodynamics based on the defect Gibbs energy calculated from Wendling-Suter model. For PHGP and PHPA, the comonomer units have better miscibility in the case of the incorporation of shorter unit into the longer unit crystal than the opposite case. By contrast, in the case of PHGA, the HG and HA units are perfectly miscible in a same crystal lattice with only a little difference in crystal cell dimensions due to the identity of chain conformation of HG and HA units during packing into the crystal lattice. Finally, a model of crystal lattice structure of copolyesters was proposed to better understand the difference in cocrystallization miscibility effect of comonomers between isodimorphism and isomorphism.