The Klein–Gordon equation with equal scalar and vector potentials [Formula: see text] describing the dynamics of a three-dimensional under the modified Coulomb plus inverse-square potential is considered, in the symmetries of noncommutative quantum mechanics (NCQM), using Bopp’s shift method. The new energy of [Formula: see text]th excited state [Formula: see text] is obtained as a function of the shift energy [Formula: see text] and [Formula: see text] is obtained via first-order perturbation theory in the three-dimensional noncommutative real space (NC: 3D-RS) symmetries instead of solving modified Klein–Gordon equation (MKGE) with the Weyl–Moyal star product. It is found that the perturbative solutions of discrete spectrum depended by the Gamma function, the discreet atomic quantum numbers [Formula: see text] and the potential parameters (A and B), in addition to noncommutativity parameters ([Formula: see text] and [Formula: see text]), which are induced with the effect of (space–space) noncommutativity properties.