In this paper, we will introduce a control strategy based on the permanent magnet linear synchronous motor (PMLSM) container transfer system using soft-computing algorithm. Linear motor-based container transport system (LMCTS) is horizontal transfer system for the yard automation, which has been proposed to take the place of automated guided vehicle in the maritime container terminal. LMCTS is considered as that the system is changed its model suddenly and variously by loading and unloading container. The proposed control system is consisted of two DR-FNNs that act the role of controller and system emulator. Consequently, the system had the predictable structure and an ability to adapt for a huge variation of rolling friction, detent force, and sudden changes of its weight by loading and unloading.