Aiming at 6-DOF virtual-axis machine tool driven by permanent magnetic linear synchronous motor (PMLSM)，a control scheme on rotor acceleration was presented based on neural network position servo controller. In order to overcome the influence of the coupling force between links, which have a strong affection to rotor acceleration, the load disturbance and coupling force have been integrated and was regarded as the dynamic parameters' variation of PMLSM, and the equivalent parameters were online observed by observer and adjusted by neural network position servo controller, the errors of the speed and position were decreased ahead. The controller has the advantages of simple structure, convenient weights adjusting, small calculation and fast response, etc. The simulation results verified that the tracking control for the position, speed and acceleration of each link was attained, and the system is robust to uncertain factors.