Many industrial machines are operated along a simple motion trajectory such as a trapezoidal or S-curve acceleration/deceleration trajectory. This paper presents a motion trajectory generation method that suppresses the residual vibrations of such machines. First, we consider a residual vibration problem for a gantry-type crane that is widely used in industrial factories. The dynamics of the crane system is represented by a simple set of differential equations. Assuming that only a simple motion trajectory can be applied to an industrial controller, we propose a motion trajectory generation method that suppresses the residual vibration, which increases the production takt time. Simulation and experimental results demonstrate the effectiveness of the proposed method.