We report a theoretical study based on density functional theory (DFT) on the geometric and electronic structure, linear optical and second-order nonlinear optical properties of a series of new inorganic–organic hybrid hexamolybdate–organoimido–(car)boranes. By the incorporation of borane/carborane at the end of the phenyl ring of the organoimido segment, the studied systems show excellent nonlinear optical (NLO) response than the organoimido-substituted hexamolybdate. The computed static first hyperpolarizability βvec value of [Mo6O18(NC8H8)(B12H11)]4− (II) is largest, −167.2 × 10−30 esu, and a higher βvec value of [Mo6O18(NC8H8)(C2B10H11)]2− (III-2p) is 58.6 × 10−30 esu. Moreover, the time-dependent (TD)DFT calculation illustrates that the maximum absorption, which is helpful for the large NLO responses, is mainly assigned to the charge transfer (CT) from (car)borane and organoimido segment to the hexamolybdate cluster. The density of density (DOS) calculations further illustrate the excitation from valence orbitals of boron atoms to that of Mo and O atoms in hexamolybdate can be responsible for larger NLO responses. The linear and nonlinear optical properties of species III both vary with the position of the vertex on the carborane. Furthermore, the order of the βvec values is consistent with the bathochromic shift of the maximum absorption for our studied systems, and the studied systems show a wider transparency range extending into the entire visible and infrared (IR) region.