Purpose This paper aims to solve the problems of the synchronization between branches and the uncertainties such as joint friction, load variation and external interference of a hybrid mechanism. The controller is used to improve the synchronization and robustness of the hybrid mechanism system and achieve both finite time convergence and chattering-free sliding mode. Design/methodology/approach First, the dynamic model of hybrid mechanism containing lumped uncertainties is formulated by the Lagrange method, and a composite error based on coupling synchronization error and the end-effector tracking error is set up in the task space. Then, by combining the finite time super twisting sliding mode control algorithm, a composite error-based finite time super twisting sliding mode synchronous control law is designed to make the end-effector tracking error and coupling synchronization error achieve better tracking performance and convergence performance. Finally, the Lyapunov stability of the control law and the finite-time convergence of the composite error are proved theoretically. Findings To verify the effectiveness of the proposed control method, simulations and experiments for the prototype system of the hybrid mechanism are conducted. The results show that the proposed control method can achieve better tracking performance and convergence performance. Originality/value This is a new innovation for a hybrid mechanism containing lumped uncertainties to improve the robustness, convergence performance, tracking performance and synchronization of the system.