In this paper, within the three-dimensional non-relativistic non-commutative phase–space (3D-NR(NCPS)) symmetries, we examined the 3D deformed Schrödinger equation (3D-DSE) using the improved Coshine Yukawa potential (ICYP) model composed from Coshine Yukawa potential (CYP) ([Formula: see text]) and other terms produced from the effect of phase–space deformation ([Formula: see text] and [Formula: see text]). For this study, the 3D-DSE in the 3D-NR(NCPS) symmetry is solved and discussed with standard independent time perturbation theory and the generalized Bopp’s shifts method. For the homogeneous (H2 and N2) and heterogeneous (LiH, ScH, and HCL) diatomic molecules, it is obtained that the improved non-relativistic energy equation and eigenfunction for the ICYP in the presence of deformation phase–space are dependent on the discrete atomic quantum numbers ([Formula: see text],m), the dissociation energy [Formula: see text], the equilibrium bond length the screening parameter [Formula: see text], the deformation phase parameters ([Formula: see text]) and the deformation space parameters ([Formula: see text]). Additionally, the thermal properties of the CYP and ICYP with 3D Schrödinger equation (3D-SE) and 3D-DSE are thoroughly examined in the three-dimensional non-relativistic quantum mechanics (3D-NR(QM)) known in the literature symmetry and 3D-NR(NCPS) symmetries, including the partition function, mean energy, free energy, specific heat, and entropy. Furthermore, we discussed particular cases of thermodynamic characteristics for the ICYP model. In our study, we have shown that all the physical values related to energy and thermodynamic properties within the framework of the 3D(NR)NCPS symmetry are equal to the corresponding values within the framework of 3D-NR(QM) symmetry known in the literature, in addition to minor effects resulting from their interaction with the topological properties of the deformed phase–space. This study has multiple applications in various domains, including atomic and molecular physics.