In this research, boron nitride (BN) acting as both nucleating agent and thermally conductive filler was melt-mixed with poly(3-hydroxybutyrate) (PHB). It was assumed that the introduction of BN not only formed thermally conductive pathways to increase the thermal conductivity of PHB, but also reduced the interfacial thermal resistance due to the interaction between BN and PHB. The assumption was confirmed by density test, morphological observation, and rheological tests. Besides, the introduction of BN improved the thermal stability of PHB, as well. Poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P3,4HB) was introduced as a comparison with PHB to illustrate the effect of crystallinity on the thermal conductivity of PHB/BN composites. According to the DSC tests, BN was proved to be a good nucleating agent for both PHB and P3,4HB. As the wide-angle X-ray diffraction analysis results showed that the crystal structure of PHB/BN and P3,4HB/BN composites was the same, the reason that the thermal conductivity of PHB/BN composites was higher than that of P3,4HB/BN composites at all BN levels was mainly because of the difference of the degree of crystallinity.