The deformed Klein-Gordonequation has been solved in three-dimensional extended relativistic quantum mechanics (3D-ERQM) symmetries for the improved modified Yukawa-Kratzer potential (IMYKP) model under the influence of the deformation space-space symmetries. The new relativistic energy eigenvalues were calculated using the parametric Bopp’s shift method and standard perturbation theory in addition to the approximation scheme suggested by Greene and Aldrich for the inverse square terms. The new relativistic energy eigenvalues of (LiH, HCl, CO and H2) molecules under the IMYKP model it was shown to be sensitive to the atomic quantum numbers (j, l, s, m), mixed potential depths (V0, De, re), the screening parameter’s inverse α and noncommutativity parameters (Θ,τ ,χ). In addition, we analyzed the nonrelativistic energy values by applying the well-known transmission rules known in the literature. In addition, we studied many special cases useful to researchers in the framework of the new extended symmetries, such as the improved modified Kratzer potential, the improved generalized Kratzer potential, the improved Kratzer potential, the improved modified Kratzer plus screened Coulomb potential, the improved Hellmann potential, the improved Yukawa potential, and improved inversely square Yukawa potential. We noticed that these particular results are identical to our previous work and other known works in the literature. The study is further extended to calculate the mass spectra of mesons of charmonium (cc) and bottomonium (bb) within the framework of the IMYKP model in three-dimensional extended non-relativistic quantum mechanics (3D-ENRQM) symmetries.