We report the investigation of the size evolution of lattice dynamics in spin crossover coordination nanoparticles of [Fe(pyrazine)(Ni(CN)4)] through nuclear inelastic scattering (NIS) measurements. Vibrational properties in these bistable molecular materials are of paramount importance and NIS permits access to the partial vibrational density of states in both spin states [high spin (HS) and low spin (LS)] from which thermodynamical and mechanical properties can be extracted. We show that the size reduction leads to the presence of inactive metal centers with the coexistence of HS and LS vibrational modes. The confinement effect has only weak impact on the vibrational properties of nanoparticles, especially on the optical modes which remain almost unchanged. On the other hand, the acoustic modes are much more affected which results in the increase of the vibrational entropy and also the Debye sound velocity in the smallest particles (<10 nm) in both spin states. This stiffening may be due to the elastic surface stress exerted by the external environment. An evidence of the influence of the host matrix on the vibrational properties of the nanoparticles is also highlighted through the matrix dependence of the sound velocity.