The crystal structures of poly(hexamethylene sebacate-co-hexamethylene adipate), P(HSe-co-HA), copolymers have been studied with Fourier transformation infrared spectroscopy (FTIR) and X-ray fiber diffraction. All characteristic FTIR absorption bands of the crystals of HSe and HA comonomers are present in all copolymers, and each copolymer has only one melt temperature, which supports that P(HSe-co-HA) copolymers cocrystallize in a whole range of comonomer compositions. In addition to peak shift, some new diffraction peaks were observed in X-ray fiber diffraction patterns of the copolymers, which correspond to new crystals with different unit cells from those of the homopolymers. The crystal structures of the copolymers were analyzed, which varied with the composition of HA and HSe comonomers. Interestingly, the lattice constants c of P(HSe-co-20 mol % HA) and P(HSe-co-35 mol % HA) crystals are even larger than those of either homopolymers, which implies a new length scale may be induced in the random copolymers. This supports the formation of new crystals instead of normal lattice distortion.