Abstract Structure and dynamics of hydrogen bonded organic ferroelectric CBDC (1-cyclobutene-1,2-dicarboxylic acid, C₆H₈O₄) have been investigated using inelastic neutron scattering (INS) spectroscopy and first principles lattice dynamics. Vibrational modes of O–H–O bending, related with two different types of hydrogen bonds, inter and intra-molecular, are manifested as two sets of doublets in the range of 900–1400 cm⁻¹ in the INS spectrum. First principles density functional theory (DFT) is used to assign these doublets to out-of-the-plane and in-plane vibrations of these two types of O–H—O bending modes. Correlating structure and dynamics we find that although the local structures of the hydrogen bonded protons are similar, their medium range order may influence their vibrational frequencies. Vibrational modes of non-hydrogen bonded protons also are assigned separately in the spectrum. Comparing the calculated and the experimental INS spectra it is predicted that hydrogen bonded O–H bonds are more anharmonic than non-hydrogen bonded C–H bonds. From the calculated Born effective charge tensor it is predicted that inter-molecular hydrogen bonds contribute more to the ferroelectric polarisation of CBDC than intra-molecular ones. A large LO-TO splitting of the O–H stretching mode at 2471 cm⁻¹ is identified with the mode that has significant contribution to the ferroelectric polarisation. As this mode is sensitive to long range Coulomb interactions and is responsible for ferroelectric properties of the material, vibrational spectroscopy combined with DFT calculations is proposed as a characterisation tool to investigate ferroelectric properties in the CBDC molecular crystal.