Abstract. In this work, an analytical expression for the nonrelativistic energy spectrum of some diatomic molecules was obtained through the Bopp's shift method in the noncommutative (NC) two-dimensional real space-phase symmetries (NC: 2D-RSP) with a new modified Kratzer-type potential (NMKP) in the framework of two infinitesimal parameters θ and θ due to (space-phase) noncommutativity, by means of the solution of the noncommutative Schrödinger equation. The perturbation property of the spin-orbital Hamiltonian operator and new Zeeman effect of twodimensional system are investigated. We have shown that, the new energy of diatomic molecule is the sum of ordinary energy of modified Kratzer-type potential, in commutative space, and new additive terms due to the contribution of the additive part of the NMKP. We have shown also that, the group symmetry of (NC: 2D-RSP) reduce to new sub-group symmetry of NC two-dimensional real space (NC: 2D-RSP) under new modified Kratzer-type interactions.