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Simulation is the most viable solution for the functional verification of system-on-chip (SoC). The acceleration of simulation with multi-field programmable gate array (multi-FPGA) emulator is a promising method to comply with the increasing complexity and large gate capacity of SoC. Time multiplexing of interconnection wires is the inevitable solution to solve the pin limitation problem that limits the gate utilization of FPGAs and speed of multi-FPGA simulation accelerators. The most time-consuming factor of multi-FPGA simulation acceleration is the synchronization time between a software simulator and a multi-FPGA system and the inter-FPGA synchronization time. This paper proposes a performance-driven signal synchronization mechanism for a simulation accelerator with multiple FPGAs using time-multiplexed interconnection. The event-based signal synchronization optimizes the synchronization time between a software simulator and the multi-FPGA system as well as the synchronization time among FPGAs. The synchronization time among FPGAs is optimized by circuit partitioning considering the signal probability, net dependency reduction, and efficient net clustering to reduce addressing overhead. The synchronization time between the software simulator and the multi-FPGA system is also optimized by exploiting the event probability of primary nets. Experiments show that the synchronization time is reduced to 6.2-9.8% of traditional mechanisms.