Magnetic clusters have attracted great attention and interest due to their novel electronic properties, and they have potential applications in nanoscale information storage devices and spintronics. The interaction between magnetic clusters and substrates is still one of the challenging research focuses. Here, by using the density functional theory (DFT), we study the structural stability and magnetic properties of iridium clusters (Irn, n = 3–5) adsorbed on two-dimensional (2D) substrates, such as graphene and hexagonal boron nitride (hBN). We find that the most favorable configurations of free Irn clusters change when adsorbed on 2D substrates. In the meantime, the magnetic moments of the most stable Irn reduce to 53% (graphene) and 23.6% (hBN) compared with those of the free−standing ones. Interestingly, about 12-times enlargement on the magnetic anisotropy energy can be found on hBN substrates. These theoretical results indicate that the cluster–substrate interaction has vital effects on the properties of Irn clusters.