We systematically analyze the integrability of a Pauli system in Lorentz violating background at the non-relativistic level both in two- and three-dimensions. We consider the non-relativistic limit of the Dirac equation from the QED sector of the so-called Standard Model Extension by keeping only two types of background couplings, the vector at, and the axial vector b(mu). We show that the spin-orbit interaction comes as a higher order correction in the non-relativistic limit of the Dirac equation. Such an interaction allows the inclusion of spin degree non-trivially, and if Lorentz violating terms are allowed, they might be comparable under special circumstances. By including all possible first-order derivative terms and considering the cases a not equal 0, b not equal 0, and b(0) not equal 0 one at a time, we determine the possible forms of constants of motion operator, and discuss the existence or continuity of integrability due to Lorentz violating background.