NCN pincer palladium(II) complexes bearing a 6-ethynyl-1-octyluracil moiety were designed by the combination of an NCN pincer palladium(II) complexes as an organometallic compound and a uracil derivative as a nucleobase to afford bioorganometallic compounds. The reaction of the NCN pincer ligand with Pd(dba)2 (dba = dibenzylideneacetone) led to the formation of the NCN pincer palladium(II) complex Pd-Br. The crystal structure of the cationic complex Pd-MeCN, which was prepared by the treatment of Pd-Br with AgOTf (OTf = trifluoromethanesulfonate) in acetonitrile, revealed that a dimeric structure formed through intermolecular hydrogen bonds between the uracil moieties of two independent molecules. The self-assembly properties of the NCN pincer palladium(II) complexes were found to depend on the ancillary ligands. Each hydrogen-bonded dimer was connected through an intermolecular hydrogen-bonding bridge between the coordinated water molecule and the triflate anion in the cationic complex Pd-H2O. Intermolecular hydrogen bonding between the uracil moiety and the triflate anion bound to the palladium center was observed in the NCN pincer palladium(II) complex Pd-OTf, although a dimeric structure between the uracil moieties was formed in the NCN pincer palladium(II) complex Pd-O2CCF3, which was obtained by the abstraction of the bromide ion from Pd-Br with AgO2CCF3.