Herein, differences in the intermolecular interactions and flexibility between poly(ethylene terephthalate) (PET) and poly(butylene terephthalate) (PBT) are studied by far-infrared, terahertz (THz), and low-frequency Raman spectroscopy and quantum chemical calculations (QCCs). Interatomic distance calculations based on the reported crystal structures and natural bond orbital analysis indicate that PBT exhibits intermolecular hydrogen bonding between a C=O group and a CH2 group in the adjacent molecular chains, while PET does not have such hydrogen bonding. The results of infrared measurements also suggest that the C=O and CH2 groups of PBT are involved in intermolecular hydrogen bonding. Both PET and PBT show a THz band at around 113 cm(-1) and a Raman band at around 111 cm(-1). These bands indicate different thermal behaviors of PET and PBT. The results of QCCs performed using the Cartesian coordinate tensor transfer method suggest that these bands of PBT include the CH2 bending mode, while those of PET have only a small contribution from the corresponding mode. These differences in the thermal behavior and vibrational modes of the 113 cm(-1) bands can be possibly attributed to the difference in flexibility between PET and PBT due to the different number of CH2 groups. In addition, these bands of PBT seem to reflect the intermolecular C=O center dot center dot center dot H-C hydrogen bonding. Therefore, it may be concluded that the difference in the number of CH2 groups causes the difference in the flexibility of the molecular chains between PBT and PET and the existence or non-existence of intermolecular C.O center dot center dot center dot H-C hydrogen bonding. It is worth noting that THz and low-frequency Raman spectroscopy can clearly reveal the difference in flexibility. It is also very likely that both the flexibility of the molecular chains and the intermolecular hydrogen bonding affect the difference in the crystallization rate between PET and PBT.