Based on the atomic local structure, a nanocrystalline material is separated into two parts: inner grains and grain boundaries. Molecular dynamics simulations have been performed to study the difference in their vibrational properties in nanocrystalline nickels. The results obtained reveal that a similar phonon frequency softening as in the perfect lattice mainly focuses on grains in nanocrystalline materials, and for the grain boundary part there is no obvious change in the vibrational density of states in the temperature range 300–900 K, especially in the lower frequency range. Comparing with conventional crystals, the higher specific heat and vibrational entropy, and lower vibrational free energy with decreasing mean grain size, result from the high proportion of grain boundaries in nanocrystals. In addition, the composite model provides a good description of the contributions of grain and grain boundary phases to thermodynamic quantities. Supposing the nanocrystalline material can be treated as a composite composed of grain and grain boundary network, the vibrational thermodynamic quantities of the system can be well determined from the proportion of grain boundaries and the corresponding thermodynamic quantities of grain and grain boundary parts. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)