Industrial control of dual-drive moving gantry stage robots is usually achieved by two independent position controllers. This control structure does not take into account the mechanical coupling between the two actuators that leads to a reduction of the overall performances. In this paper, a physical dynamic lumped parameters model of an industrial robot based on structural, modal, and finite element method analysis is proposed, experimentally identified and validated. Then, using simple inversion rules of the causal ordering graph formalism, a control structure is deduced in a systematic way. The solution is finally simulated and shows that it is possible to obtain better performances than the industrial control.