This paper presents an innovative flexible assembly system – hybrid assembly cell lines (HACL) to adapt to small batch, high product variety and dynamic demands. HACL provides specially designed trolleys for assembly operations, materials and tools to form the workstations flexibly and quickly at low reconfiguration cost. To conduct accurate and effective control for this complex assembly system, this paper presents a modified Graduation-inspired Manufacturing System (GMS), a recently proposed new card-based control system. GMS for HACL designs three kinds of tickets and the ticketing mechanism to absorb the uncertainties of HACL. Job tickets are for workload control and synchronization of part deliveries; setup tickets are for cell line formation and synchronization of resources of tools and machines; operation tickets are for production execution and synchronization of workers and operations in cell lines. GMS for HACL develops Internet of Things-enabled (IoT-enabled) architecture for managing the smart tickets to achieve automatic and intelligent interoperability between GMS and the physical workstations of HACL. This work designs synchronization mechanism based on specific model and genetic algorithm to synchronize manufacturing resources under GMS for HACL