In this paper, a new organic-inorganic hybrid, 4-methylbenzyl-2-aminopyridinium tetrachloromanganate(II)[4-MeBz-2-NH2Py]2[MnCl4](1), was synthesized and characterized. The single crystal X-ray diffraction analysis showed that the as-prepared hybrid crystallizes in triclinic space group P-1 and consists of two [4-MeBz-2-NH2Py]+ cations and a tetrahedral [MnCl4]2− anion. The emission spectrum and excitation spectrum appear at 520 nm and 343 nm, and the latter was consistent with the fluorescence color of the crystal illuminated by a 365 nm UV light. The intermolecular energy, the energy gap between the HOMO and LUMO orbitals, and the first hyperpolarizability was predicted by the DFT calculations. The low energy gap (1.28 eV) explained the eventual charge transfer interactions taken place between the [MnCl4]2− anion and [4-MeBz-2-NH2Py]+ cations. The first hyperpolarizability (βtot) was more than 3600 times that of the standard KDP crystal, proving that the title hybrid is a superior material for NLO application. In addition, the hybrid exhibits superior bactericidal activity for S. aureus and E. coli.