Segment assembling is one of the principle processes during tunnel construction using shield tunneling machines. The segment erector is a robotic manipulator powered by a hydraulic system to assemble prefabricated concrete segments onto the excavated tunnel surface. Nowadays, automation of the segment erector has become one of the definite developing trends to further improve the efficiency and safety during construction; thus, closed-loop motion control is an essential technology. Within the segment erector, the lifting gantry is driven by dual cylinders to lift heavy segments in the radial direction. Different from the dual-cylinder mechanism used in other machines such as forklifts, the lifting gantry usually works at an inclined angle, leading to unbalanced loads on the two sides. Although strong guide rails are applied to ensure synchronization, the gantry still occasionally suffers from chattering, “pull-and-drag”, or even being stuck in practice. Therefore, precise motion tracking control as well as high-level synchronization of the dual cylinders have become essential for the lifting gantry. In this study, a complete dynamics model of the dual-cylinder lifting gantry is constructed, considering the linear motion as well as the additional rotational motion of the crossbeam, which reveals the essence of poor synchronization. Then, a two-level synchronization control scheme is synthesized. The thrust allocation is designed to coordinate the dual cylinders and keep the rotational angle of the crossbeam within a small range. The motion tracking controller is designed based on the adaptive robust control theory to guarantee the linear motion tracking precision. The theoretical performance is analyzed with corresponding proof. Finally, comparative simulations are conducted and the results show that the proposed scheme achieves high-precision motion tracking performance and simultaneous high-level synchronization of dual cylinders under unbalanced loads.