Biodegradable polyhydroxyalkanoate (PHA) based polymer nanocomposite filled with nanoscale carbon fibers (CFs) were prepared by electrospinning. To enhance the processability and thermal properties of the composites, the carbon fibers were treated with chemical reagents, namely n-octanol, silane coupling agent (KH-550), and nitric acid (HNO3). The SEM result shows that the composite fibers with nitric acid treated CFs have the finest diameters and many uniform thickness distributions. All surface treatments on carbon fibers have increased the glass transition temperatures and crystallinities of the composites, with nitric acid treatment being the best. The improvements further depended on the volume fraction of the carbon fibers.