During the synchronous operation of the double-container, the double-lift overhead cranes suffer from the perturbation of system internal parameters, friction and external unknown disturbances. To address the impact of the above-mentioned negative factors, based on the mathematical model of induction motor and the coupled dynamics model of double-container, this paper proposes a synchronous control method combining variable gain extended state observer and nonlinear time-varying sliding mode surface for the synchronous coordination control of double-lift overhead cranes system. The load dynamics model of the double-container interlocking mode is established. Then, a nonlinear time-varying sliding mode surface is designed by means of nonlinear function and dynamic exponential term, which effectively speeds up the convergence of the system state and enhances the robustness of the system. Furthermore, the design adaptive reaching law is used to weaken the unwanted chattering and improve the performance of the controller. At the same time, the designed variable gain extended state observer estimates the aggregated disturbances in the system and then compensates them into the controller. The Lyapunov stability theory is used to prove the stability of the control system. The simulation experiments illustrate the effectiveness of the proposed synchronization control scheme.