Graphene with defects is a vital support material since it improves the catalytic activity and stability of nanoparticles. Here, a density functional theory study was conducted to investigate the stability, energy, and reactivity properties of NinPdn (n = 1–3) clusters supported on graphene with different defects (i.e., graphene with monovacancy and pyridinic N-doped graphene with one, two, and three N atoms). On the interaction between the clusters and graphene with defects, the charge was transferred from the clusters to the modified graphene, and it was observed that the binding energy between them was substantially higher than that previously reported for Pd-based clusters supported on pristine graphene. The vertical ionization potential calculated for the clusters supported on modified graphene decreased compared with that calculated for free clusters. In contrast, vertical electron affinity values for the clusters supported on graphene with defects increased compared with those calculated for free clusters. In addition, the chemical hardness calculated for the clusters supported on modified graphene was decreased compared with free clusters, suggesting that the former may exhibit higher reactivity than the latter. Therefore, it could be inferred that graphene with defects is a good support material because it enhances the stability and reactivity of the Pd-based alloy clusters supported on PNG.