We have investigated the crystallization of a series of bio-based polyesters made from isohexides [isomannide (M) or isosorbide (S)] and aliphatic dicarboxylic acids (Mk or Sk with k = 4, 5, 6, 8, 10, 12, where k is the carbon number of dicarboxylic acid units). The effects of stereoisomerism of isohexide units (M or S) and chain length of dicarboxylic acid units (k) on the crystallization of the polyesters were systematically examined. A crystalline nature of M4, M10, M12, S10, and S12 was confirmed by differential scanning calorimetry, wide-angle X-ray diffraction, and polarized optical microscopy. Especially, we performed detailed studies on the crystalline hierarchical structure and crystallization behavior of the crystalline polyesters with long dicarboxylic acid units (k ≥ 10). The larger k gave a higher crystallinity for both Mk and Sk (k = 10, 12), while a difference in crystallinity between Mk and Sk was not so large. The right-handed 2/1 helical conformation of M12 was proposed on the basis of the fiber diagram, infrared progression bands, and conformational analysis. The equilibrium melting temperatures of Mk and Sk (k = 10, 12) were determined to ca. 100 °C using the solvent-annealed samples. The crystallization rate drastically increased with increasing k, and the crystallization of Sk was faster than that of Mk.