Graphdiyne (GDY) is a newly discovered 2D carbon allotrope, widely used as a support for heterogeneous transition metal catalysts. We investigated the binding, electronic structure, diffusion mechanisms and aggregation possibilities of mono-dispersed Ir atoms on GDY by extensive first-principles based calculations. The binding of Ir atoms on GDY can be up to -4.84 eV when the Ir atom is trapped in the C18 ring interacting with 2 adjacent diyne moieties connected to the same benzene ring. The diffusion of Ir atoms along the diyne moiety is quite facile with barriers less than 0.89 eV; the highest barrier for Ir diffusion into the C18 ring is 0.10 eV, whereas inter/intra-C18 ring diffusion is limited by a barrier of 1.64 eV, thereby leading to a dominant population of Ir atoms trapped in the C18 rings. The electronic structure of small Ir clusters was also investigated. Though the formation of Ir-Ir bonds is exothermic and thermodynamically favorable, which may, in some circumstances, even overwhelm the formation of interfacial Ir-C bonds, aggregation of Ir atoms into clusters is limited by the high energy barrier of inter/intra C18 ring diffusion. We propose that aggregation of Ir atoms into clusters may be initiated by shifting the diffusion thermodynamics deliberately and expect the finding may help to understand the stability and evolution of GDY based single atom catalysts.