We have observed, for the first time, a heterogeneous spatial distribution of crystalline polymorphs in a single electrospun polymer nanofiber. Two crystalline polymorphs of PHBHx, the thermodynamically stable a-form consisting of chains with a 2(1) helical conformation and the metastable beta-form consisting of chains with a planar zigzag conformation, are spatially distributed as a core-shell structure composed of an alpha-form-rich core and a beta-form-rich shell. In addition, it was found that the thickness of the shell is independent of the fiber diameter. The characterization of crystalline polymorphic distribution in individual nanofibers has been made possible by utilizing a technique combining atomic force microscopy (AFM) and infrared spectroscopy (IR), which simultaneously provides the nanoscale spatial resolution and crystalline phase specificity. Based on the experimental results, a possible generation mechanism of this polymorphic heterogeneous core-shell structure is proposed. The implications of this core-shell model on fiber properties are also discussed.