The gate utilization of FPGAs and speed of emulation in multi-FPGA system are limited by the interconnection architecture and the number of pins. The time-multiplexing of interconnection wires is required for multi-FPGA systems incorporating several state-of-the-art FPGAs. This article proposes a circuit partitioning algorithm called SCheduling driven Algorithm for TOMi (SCATOMi) for multi-FPGA systems with interconnection architecture called Time-multiplexed, Off-chip, Multi-casting interconnection (TOMi). SCATOMi improves the performance of the TOMi architecture by limiting the number of inter-FPGA signal transfers on the critical path and considering the scheduling of inter-FPGA signal transfers. The performance of the partitioning result of SCATOMi is 5.5 times faster than traditional partitioning algorithms. Experiments on architecture comparison show that, by adopting the proposed TOMi interconnection architecture along with SCATOMi, the pin count is reduced to 15.2–81.3% while the critical path delay is reduced to 46.1–67.6% compared to traditional architectures.