Silk fibroin (SF) fiber from the Antheraea pernyi silkworm was treated with a 1.23 N iodine-potassium iodide ($I_2-KI$) aqueous solution, and the structure and physical properties were investigated to clarify the effects of the iodine treatment. The noticeably high weight gain value of SF fiber, about 25 wt% was attributed to the absorption of polyiodide ions in the form of $I_3{^-};and;I_5{^-}$. Fourier transform infrared spectroscopy and X-ray diffraction measurements suggested that polyiodide ions mainly entered the amorphous region. In addition, a new sharp reflection on the meridional direction, corresponding to a period of $7.0{AA}$, was observed and indicated the possibility of the formation of mesophase structure of ${eta}$-conformation chains. Dynamic viscoelastic measurements showed that the damping tan ${delta}$ peak at $270^{circ}C$ gradually shifted to lower temperature in the iodinated SF fibers, suggesting an enhancement of the molecular motion of the fibroin chains induced by the presence of polyiodide ions. With heating above $254^{circ}C$, the iodine component introduced intermolecular cross-linking of SF, and the melt flow of the sample was inhibited. The thermal decomposition stability of fibroin molecules was greatly enhanced by iodine treatment.