Combining in a synergic way inorganic and organic matter at nanometre level has become a key research pathway for nanoelectronics, light harvesting, energy storage or sensing. Herein, we demonstrate the nanoscale ordering at room temperature of a two-dimensional hybrid assembly combining a long-range ordered array of Pd nanoparticles (NPs) with perylene molecules. The ordering, driven by the periodic superstructure of the Al2O3 ultrathin layer support, has been achieved for 0.9 nm diameter NPs and flat-lying molecules with a 2:1 perylene:NP relative ratio. At larger NP size and perylene coverage, molecules tilt up on alumina and adsorb on NPs. Combined near-field microscopy and optical spectroscopies provide a detailed understanding of the structural properties as a function of NP size and molecular coverage. This hybrid assembly opens the way to study at the molecular level the optical and electronic properties resulting from the coupling of organic molecules and nanoparticles using multi-scale surface sensitive techniques.