Surface ligands on metal nanomaterials play a crucial role in the controlled synthesis of metal nanoparticles with specific size and morphology. However, the detailed molecular-level structures of surface ligands are difficult to be determined by conventional characterizations, leading to our poor understanding over the effects of surface ligands on the chemical properties of metal nanomaterials. Benefiting from the development of metal nanoclusters and other model nanomaterials, increasing research effort has been devoted to revealing the detailed coordination structure of surface ligands on metal nanomaterials and their catalytic effects. The coordination of organic molecules on the metal surface can not only regulate the electronic structure of the surface metal, but also alter the periodic structure of the surface atoms. Moreover, the assembling of surface organic ligands can create 3D spatial structure on the metal surface for manipulating the interaction strength and configuration of reactants and intermediates with the catalytic surface. The interface created by having organic ligands modify metal surface can also lead to the formation of new catalytic sites for changing the catalytic reaction pathways to improve the catalytic activity and selectivity. The assembling effects of surface ligands on metal nanomaterials make them exhibit advantages of heterogeneous catalysis and homogeneous catalysis.