We explore the effects of interlayer vacancy defects on the vibrational properties of Bernal (AB) stacking bilayer armchair graphene nanoribbons (BiAGNRs) using the forced vibrational method. It is observed that the Raman active longitudinal optical (LO) phonon of BiAGNR is shifted downward with the decrease of the ribbon width and an increase of the vacancy concentrations. We find that vacancies induce some new peaks in the low frequency regime of the phonon density of states. Our calculated typical mode patterns elucidate that the localized transverse optical phonon at the K-point is shifted towards the defect sites from the edges with increased vacancy concentrations. In addition, the impact of defect induced phonon modes on the specific heat capacity and thermal conductivity of BiAGNRs are discussed. These results present a new way of understanding the heat dissipation phenomena of graphene-based high-performance nanodevices and to clarify the Raman and the experiments related to the phonon properties.