In this paper, we consider Morse theory for perturbed Dirac-harmonic maps into flat tori. We show that Morse homology can be defined for some classes of perturbations, and that it is determined by a homotopy type of the perturbations. We also give an explicit computation of the homology. As an application, we give a lower bound on the number of perturbed Dirac-harmonic maps in a given component for some classes of perturbations.