A novel phenoxy-bridged trinuclear nickel(II) complex [Ni₃(μ-L)₂(bipy)₃](1) (where H₃L= (E)-2-hydroxy-N-(2-hydroxy-3,5-diiodophenyl)-3,5-diiodobenzohydrazonic acid, bipy = 2,2′-bipyridyl) has been designed and synthesized as a potential antivirus drug candidate. The trinuclear Ni(II) complex [Ni₃(μ-L)₂(bipy)₃](1) was fully characterized via single crystal X-ray crystallography. The unique structure of the trinuclear nickel(II) complex crystallized in a trigonal crystal system with P3₂21 space group and revealed distorted octahedral coordination geometry around each Ni(II) ion. The X-ray diffraction analysis established the existence of a new kind of trinuclear metal system containing nickel(II)–nickel(II) interactions with an overall octahedral-like geometry about the nickel(II) atoms. The non-bonded Ni–Ni distance seems to be 3.067 and 4.455 Å from the nearest nickel atoms. The detailed structural analysis and non-covalent supramolecular interactions are also investigated by single crystal structure analysis and computational approaches. Hirshfeld surfaces (HSs) and 2D fingerprint plots (FPs) have been explored in the crystal structure to investigate the intermolecular interactions. The preliminary analysis of redox and magnetic characterization was conducted using cyclic voltammetry measurements and a vibrating sample magnetometer (VSM), respectively. This unique structure shows good inhibition performance for SARS-CoV-2, Omicron and HIV viruses. For insight into the potential application of the Ni(II) coordination complex as an effective antivirus drug, we have examined the molecular docking of the trinuclear Ni(II) complex [Ni₃(μ-L)₂(bipy)₃](1) with the receptor binding domain (RBD) from SARS-CoV-2 (PDB ID: 7MZF), Omicron BA.3 variant spike (PDB ID: 7XIZ), and HIV protease (PDB ID: 7WCQ) viruses. This structure shows good inhibition performance for SARS-CoV-2, Omicron S protein and HIV protease viruses; the binding energies (ΔG) and the respective K_i/K_d (inhibition/dissociation constants) correlation values are −8.9 (2.373 μM or 2373 nM), −8.1 (1.218 μM or 1218 nM) and −7.9 (0.874 μM or 874 nM), respectively. The results could be used for rational drug design against SARS-CoV-2 Omicron variant and HIV protease viruses.