The coverage and temperature-dependent nucleation behaviors of the Gd@C82 metallofullerenes on Cu(111) have been studied by low-temperature scanning tunneling microscopy (LT-STM) in detail. Upon molecular deposition at low temperature, Gd@C82 molecules preferentially decorate the steps and nucleate into single layer islands with increasing coverage. Further annealing treatment leads some of the Gd@C82 molecules to assemble into bright and dim patches, which are correlated to the adsorption induced substrate reconstruction. Upon sufficient thermal activation, Gd@C82 molecules sink into the Cu(111) surface one-copper-layer-deep, forming hexagonal close-packed molecular islands with intra-molecular details observed as striped patterns. By considering the commensurability between the Gd@C82 nearest-neighbor distance and the lattice of the underlying Cu(111), we clearly identified two kinds of in-plane molecular arrangements as (√19 × √19)R23.4° and (√19 × √19)R36.6° with respect to Cu(111). Within the assembled Gd@C82 molecular, island molecules with dim—bright contrast are spatially distributed, which may be modulated by the preexisted species on Cu(111).