Taking the Pendubot moving in vertical plane motion as the research object, a trajectory planning and control method based on the intelligent optimization algorithm is proposed to solve the problem that it is difficult to transit from swing-up area to balance area in the control process. Firstly, a forward trajectory from the initial angle to the middle angle and a reverse trajectory from the middle angle to the target angle are planned for the Pendubot. The unactuated link moves under the action of system coupling relation, and the corresponding end point of the Pendubot moves to the relevant position. The genetic algorithm is used to optimize the trajectory parameters, so that the forward and reverse trajectories are combined into a driving link trajectory from the initial angle to the target angle, and the corresponding Pendubot terminal trajectory moves from the vertical downward balance position to the vertical upward balance position. Then, a tracking controller is designed to make the driving link move to the target angle along the optimized trajectory of the driving link, the end point of Pendubot also moves to the vertical upward balance position in virtue of the existence of coupling relationship. Due to the influence of gravity, it is difficult for the Pendubot to stabilize the end point at the vertical upward position for a long time. Thus, the stabilization controller is designed to keep the end point stable at the vertical upward balance position. Finally, the effectiveness of the proposed method is proved by simulation experiments, the advantages of this method in singularity avoidance, controller design and control effect are illustrated by comparison.