A continuum mesoscopic model of a Moiré-regulated self-assembly of metal clusters on graphene is developed. Computations for Pt, Ni and Pb show the clusters assembly at the Moiré cells centers, starting from a spatially non-uniform submonolayer coverage over a large graphene area. Differences in the efficiency of a cluster self-assembly for three chosen metals are highlighted across three typical values of the initial coverage and for three temperature regimes. Model enhancement by incorporation of an adsorption potential on graphene leads to a significantly faster self-assembly of the clusters and has a transient impact on the cluster morphologies.