Metal-organic nanostructures on surfaces have attracted considerable attention owing to their structural stability and potential applications. In metal-organic nanostructures, metal atoms are derived from the externally deposited metals or native surface atoms. Externally deposited metals are of rich diversity and depend on the targeted nanostructures. However, native surface atoms are restricted to single-crystalline metal surfaces of gold, silver, and copper, which are usually used in surface science. Metal-organic nanostructures mostly consist of Au-or Cu-coordinated motifs, while only a few consist of surface Ag atoms. Further investigation into the molecule-metal interactions is beneficial for the accurately controlled fabrication of the desired nanostructure. As for the building blocks, organic molecules coordinate with native surface atoms by M-C, M-N, and M-O bonds. The reactions of terminal alkynes or Ullmann couplings could realize the formation of C-M-C linkages. Cu and Au atoms could coordinate with molecules with terminal cyano or pyridyl groups to form N-M-N bonds. In addition, surface Ag adatoms could coordinate with phthalocyanine through Ag-N bonds. However, a comprehensive study of M-O coordination bonds is still lacking. Thus, we used hydroxyl-terminated molecules to coordinate with Ag adatoms to form metal-organic coordination nanostructures and study the O-Ag linkages. In this case, we successfully built and investigated a series of ordered structures by depositing 4,4'-dihydroxy-1,1':3',1''-terphenyl (H3PH) molecules on the Ag(111) surface by scanning tunneling microscopy. At room temperature, a close-packed ordered structure was formed by H3PH molecules through cyclic hydrogen bonds, and the repeat unit of such nanostructures contained eight H3PH molecules. Upon increasing the annealing temperature, the formation of O-Ag bond led to a change in the self-assembly pattern. When the annealing temperature was increased to 330 K, a new ordered nanostructure occurred due to the combination of O-Ag coordination and hydrogen bonds. Upon further increasing the annealing temperature to 420 K, a honeycomb structure and coexisting two-fold coordination chains appeared, which only consisted of O-Ag-O linkages. Density functional theory calculations were carried out to analyze the metal-molecule reaction pathways and energy barriers of the O-Ag-O bonds. The energy barrier of the O-Ag bond is 1.41 eV, which is less than that of the O-Ag-O linkage calculated to be 1.85 eV. The low energy barrier of the O-Ag bond and large coordination energy of the O-Ag-O linkage can be attributed to the formation of the hierarchical metal-organic nanostructure.The results obtained herein provide an effective approach for designing and building two-dimensional hierarchical structures with organic small molecules and metal adatoms on single-crystalline metal surfaces.