The performance of the acceleration/deceleration motion control algorithm directly affects the motion efficiency, motion precision and motion smoothness of the control system such as CNC machine tools and robots. The thought of constructing Sshaped curve from target requirement was proposed. In order to solve the problems existing in common sevensegment and fivesegment Sshaped curve acceleration/deceleration control algorithm, a threesegment Sshaped curve acceleration/deceleration algorithm based on the fifthorder polynomial was constructed. The motion control algorithm was simplified compared with traditional Sshaped curve acceleration/deceleration control algorithm. Its acceleration, velocity and displacement curves were all continuously differentiable so that its movement was smooth without shock and its acceleration and deceleration control efficiency was high. Through MATLAB simulation and screw hole array processing test, the algorithm has higher motion efficiency and smoothness than the traditional Sshaped curve control algorithm in the acceleration and deceleration process.