Aliphatic-aromatic biodegradable random copolyester, poly (butylene sebacate-co-butylene isophthalate) (PBSeI) was synthesized by a two step direct melt polycondensation method. This copolyester was characterized by solubility studies, viscosity measurements, infrared, 1H-NMR, 13C-NMR and thermal data. However, to be a real alternative to classical synthetic polymers and find applications, the thermal properties of biodegradable polymers have to be improved. Synthesis of nano-biocomposites, which are obtained by incorporation of nanofillers into a biomatrix, is an interesting way to create polymers with characteristic properties. In the present study, the nano-biocomposites were synthesized by dispersing different weight percentages (1, 3 and 5%) of organo-modified montmorillonite clay (OMMT) into the biodegradable polyester matrix by the solvent intercalation method. Structural characterization and thermal analysis were carried out to better understand, the relationship between the structuring of the nanofillers and the properties of nano-biocomposites. The X-ray diffraction patterns obtained for the systems confirmed the nanodispersion of the OMMT-clay in the polyester networks. The scanning electron microscopy and high resolution transmission electron microscopy analyses showed that there was no phase separation between the two components which confirmed the compatibility of polyester with the organo-modified clay system. The results show that clay incorporation improved the thermal properties of PBSeI due to the exfoliated structure of the nanocomposites formed, and thus may increase the applicability of this biodegradable polymer in different fields.