Within the framework of three-dimensional non-relativistic noncommutative quantum phase-space (3D-NRNCPS) symmetries, we study the three-dimensional deformed Schrödinger equation (3D-DSE) using the improved modified Kratzer plus generalized inverse quadratic Yukawa potential (IMK-GIQYP) and the improved modified screened Kratzer plus inversely quadratic Yukawa potential (IMSK-IQYP) models. For this consideration, the well-known generalized Bopp’s shifts method and standard perturbation theory are used to solve the DSE in the 3D-NRNCPS regime. For the homogeneous (H2, N2 and I2) and heterogeneous (CO, CH and NO) diatomic molecules, the new non-relativistic energy equation and eigenfunction for the IMK-GIQYP and the IMSK-IQYP models in the presence of deformation phase-space are obtained to be sensitive to the atomic quantum numbers ([Formula: see text] and m), the mixed potential depths ([Formula: see text] and V) and ([Formula: see text] and [Formula: see text]), the screening parameters ([Formula: see text] and [Formula: see text]), and non-commutativity parameters ([Formula: see text] and [Formula: see text]) for the IMK-GIQYP and the IMSK-IQYP, respectively. We investigate the newly obtained bound state eigenvalues of the DSE in 3D-NRNCPS symmetries using the IMK-GIQYP and the IMSK-IQYP, with appropriate adjustments made to the improved modified Kratzer potential, improved modified screened Kratzer potential, improved generalized inverse quadratic Yukawa potential model and improved inversely quadratic Yukawa potential model. Additionally, in 3D-NRNCPS symmetries, the thermal properties of the IMK-GIQYP and the IMSK-IQYP, including their partition function, mean energy, free energy, specific heat and entropy, are thoroughly examined. Significant areas, including atomic and molecular physics, find many uses for this study.