The nanophase structure of semicrystalline polymers, which determines the mechanical, thermal, and gas permeability behavior, can be quantified by thermal methods. A detailed investigation of the nanophase structure of poly[(R)-3-hydroxybutyrate] (PHB) was performed under conditions of isothermal, quasi-isothermal, and nonisothermal crystallizations. The experimental analyses revealed that the establishment of the nanophase rigid amorphous fraction (RAF) in PHB depends on the temperature at which crystallization occurs. The RAF grows in parallel with the crystal phase during quasi-isothermal crystallization at 30 °C, whereas during nonisothermal crystallization at higher temperatures, RAF starts to develop at 70 °C, in correspondence with the final stages of the crystallization process. The influence of crystallization temperature on the nanophase structure was rationalized taking into account the effect of the mobility of the entangled chain segments during the phase transition. The melting behavior was found to change after isothermal crystallization at 70 °C, revealing that complete RAF mobilization is achieved approximately at this temperature. The temperature of 70 °C could be the limit for the formation and the disappearance of rigid amorphous fraction in the PHB analyzed in the present study.