Modeling of vibrations of a rotating pendulum with working shape memory alloy rod has been performed in the frames of a microstructural model taking into account the latent heat release, absorption and the heat exchange during direct and reverse martensitic transformation. It has been shown that the influence of the latent heat, the rate of preliminary deviation of the pendulum from the equilibrium, the rate of heating and cooling can have a significant impact on the vibrations and damping characteristics of the system.