The crystalline phase of random poly(hexamethylene sebacate-co-hexamethylenc adipate) (P(HSe-co-HA)) was studied by differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) spectroscopy, wide-angle X-ray diffraction (WAXD), and small-angle X-ray scattering (SAXS). From the quantitative analysis of the comonomer composition in the crystalline phase and the finding of the change both in the WAXD patterns and in the d-spacing values of some planes in the HA composition (C-HA) of 60 mol % < C-HA < 70 mol %, the occurrence of isodimorphism was confirmed for P(HSe-co-HA). As the secondary comonomer unit content in the crystalline phase decreased with increasing crystallization temperature, it was concluded that the cocrystallization of the HSC and HA units ill the crystal of P(HSe-co-HA) is affected by kinetics. From SAXS analysis, the lamella thickness of P(HSe-co-HA) was found to rely on the comonomer unit inclusion behavior in the PHSe or PHA type crystal. Application of the Sanchez-Eby model suggests low values of excess free energy of inclusion in PHSe or PHA type crystal, indicating that the cocrystallization of HSe and HA units in the crystal of P(HSe-co-HA) is thermodynamically favored.