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Low-frequency peaks in the Raman spectra of amorphous poly(ether ether ketone) (PEEK) were investigated. An amorphous sample with zero crystallinity, as confirmed by wide-angle X-ray diffraction, was used in this study. In a previous study, two peaks were observed in the low-frequency Raman spectra of the crystallized samples. Among these, the peaks at 135 cm−1 disappeared for the amorphous sample. Meanwhile, for the first time, the peak at 50 cm−1 was observed in the crystallized sample. Similar to the peak at 135 cm−1, the peak at 50 cm−1 disappeared in the amorphous state, and its intensity increased with increasing crystallinity. The origins of the two peaks were associated with the Ph-CO-Ph-type intermolecular vibrational modes in the simulation. This suggests that the Ph-CO-Ph vibrational mode observed in the low-frequency region of PEEK was strongly influenced by the intermolecular order.