A noncentrosymmetric aluminum borate crystal, Al5BO9, was obtained via high-temperature solution method. Considering the structure diversities of Al5BO9, the single crystal structure was cautiously redetermined before the investigation. The fundamental building blocks of the structure are BO3 triangles, AlO4 tetrahedra, and AlO6 octahedra. Since Al5BO9 only consists of strong covalent B–O and Al–O bonds, it is worth investigating the structure–optical property relationship thoroughly, especially the linear and nonlinear optical properties. To gain further insight into the origin of the nonlinear optical response of Al5BO9, the electronic structure calculations, second harmonic generation (SHG)-weighted electron density, and dipole moment of polyhedra were analyzed in detail. All evidences deduced from calculated results indicate that the SHG contribution from the Al–O polyhedra is more pronounced than that of the BO3 group in Al5BO9, which is anticipated to open a window for the search and design of new inorganic materials.