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Neat polyphenylene sulfide (PPS) fiber and nano titanium-silicon dioxide-modified PPS fibers (A-PPS) were submitted to an over-temperature in air environment at 200, 220, and 240°C for 24, 192, and 360 h, respectively. Molecular and supramolecular structures were characterized by differential scanning calorimetry, X-ray diffraction, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy (XPS). The outside color of the PPS fibers turned yellow and the mechanical properties were reduced after over-temperature, but the performances of the A-PPS fibers were better than that of the neat PPS fibers. The analyses of the molecular and supramolecular structures showed that the temperatures of 200 and 220°C could not change the crystalline form but could increase the crystallinity of the PPS fibers. The crystallization temperature high-shifted and the crystallization FWHM increased after over-temperature. More significant changes at 240°C could be observed such as breaking of the macromolecular chains, mutual cross-linking, and increase of the melting enthalpy to a higher value than the complete crystallization enthalpy of PPS. Cross-linking between the benzene rings and oxidation of the S atoms did not change the PPS crystalline form but decreased the lattice constant. XPS spectra showed that the cross-linking and oxidation of the S atoms of the PPS fibers mainly came from the breaking of the C–S–C bonds, while the break ratio of the C–S–C bonds was relatively smaller in the case of the A-PPS fibers.