This work reports the synthesis of a novel diphosphopentamolybdate compound with the formula (C6H17N3)4[Co(H2O)4P2Mo5O23]2‧8·74H2O abbreviated as (H2AEP)4[CoP2Mo5]2. Characterization of this compound was carried out using various techniques, including X-ray diffraction, thermal analysis (TGA), and spectroscopies such as FT-IR, Raman, UV–visible, and fluorescence. The structural study reveals that the studied material crystallizes in the orthorhombic system Pca21 with lattice parameters of a = 18.6348(16) Å, b = 11.8613(10) Å, c = 35.074(3) Å, and volume V = 7752.5(11) Å3, and a number of formula units per primitive cell Z = 4. The crystal structure study reveals that the Strandberg anions (P2Mo5O23)6− are connected to Co(II) octahedra through the terminal oxygen atoms of the PO4 tetrahedra, creating 1-D anionic chains in the crystallographic direction [101]. The 1-(2-Aminoethyl)piperazinium (AEP) cations are located within the anionic framework to neutralize its negative charge. The magnetic characteristics of the compound were investigated by examining the temperature-dependent molecular susceptibility over the range of 2–300 K. The analysis revealed the presence of an antiferromagnetic exchange interaction. Moreover, the material's refractive index exhibited significant dispersive behavior within the visible spectrum, indicating its potential for use in visible optical communication devices. A first-principles density functional theory (DFT)-based computational study confirms the semiconducting behavior of (H2AEP)4[CoP2Mo5]2, revealing that in the ground state, high-spin octahedrally coordinated Co2+ cations exhibit a very weak antiferromagnetic coupling along the [Co(H2O)4P2Mo5O23]∞4−chains running in the crystal a direction.