Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx) scaffolds were prepared by thermally inducing phase separation (TIPS) for bone reconstruction. Scanning electron microscopy and porosity measurements were used to analyze the structure and properties of the scaffolds. The pore diameter of the scaffolds could be easily controlled by changing the quenching temperature and time. The biocompatibility was assessed by examining the proliferation and morphology of MC 3T3-E1 osteoprogenitor cells seeded on the scaffolds. Cultures grown in the presence of a source of phosphate ions showed the formation of a mineralized extracellular matrix. The results indicate that PHBHHx scaffolds prepared using TIPS are a promising candidate for bone reconstruction.