At present, many industrial carrier devices utilize linear motor sliders. However, a heavier load requires a linear motor (which is an example of a direct drive device) to get higher power, compared with a rotary motor with a ball screw slider (which is an example of an indirect drive device). In order to obtain higher power at a lower cost, a linear slider with multiple motors can be utilized, for example, a gantry type linear motor slider. Moving the gantry type slider requires two linear motors that are set up in parallel to enable synchronization control. Some conventional synchronization control methods have been proposed for the parallel twin linear slider; however, a large scaled gantry type linear motor slider has two unique problems: mechanical distortion caused by the limitations of installation environment and coupling caused by joints with low stiffness. This paper proposes a control model to solve these problems, and an identification method of each parameter. Furthermore, the effectiveness of the control model is verified by comparison with simulation results and experimental results.