The crystallization behavior of microbially synthesized poly(3-hydroxybutyrate) (PHB) and its copolymers [P(HB-co-HHx)] containing 2.5, 3.4, and 12 mol % 3-hydroxyhexanoate (HHx) comonomer and the melting of the resultant crystals were studied in detail using time-resolved small-angle X-ray scattering and differential scanning calorimetry. The polyesters were found to undergo primary crystallization as well as secondary crystallization. In-the primary crystallization, the thicknesses of the lamellar crystals were sensitive to the crystallization temperature, but no thickening was observed throughout the entire crystallization at a given temperature. The thickness of the lamellar crystals in the PHB homopolymer was always larger than that of the amorphous layers. In the copolymers, by contrast, the randomly distributed HHx comonomer units were found to be excluded from the lamellar crystals into the amorphous regions during the isothermal crystallization process. This interrupted the crystallization of the copolymer chains, resulting in the formation of lamellar crystals with thicknesses smaller than those of the amorphous layers. The lamellar crystals in the copolymers had lower electron densities compared to those formed in the PHB homopolymer. On the other hand, secondary crystallization favorably occurred during the later stage of isothermal crystallization in competition with the continuous primary crystallization, forming secondary crystals in amorphous regions, in particular in the amorphous layers between the primarily formed lamellar crystal stacks. Compared to the primarily formed lamellar crystals, the secondary crystals had short-range-ordered structures of smaller size, a broader size distribution, and a lower electron density.