Multi-FPGA boards are widely used for rapid system prototyping. Even though the prototyping is trying to reach the maximum performance, the performance is limited by the inter-FPGA communication. As the capacity per I/O for each FPGA generation is increasing, FPGA I/Os are becoming a scarce resource. The design is divided into several parts, each part's capacity fits in a single FPGA. Signals crossing design's parts located in different FPGAs are called cut nets. In order to resolve pin limitation problem, cut nets are sent between FPGAs in pipelined way using the Time-Division-Multiplexing technique. The maximum number of cut nets passing through one FPGA I/O is called the TDM ratio. There are two multiplexing architectures used for multi-FPGA based prototyping: Logic Multiplexing and ISERDES/OSERDES. In this paper, a new multiplexing architecture Multi-Gigabit Transceiver (MGT) is proposed. Experiments are done in a multi-FPGA board with the testbench LFSR to validate the achieved performance. Assume that all the FPGA I/Os used for inter-FPGA communication are MGT capable in the future. Analyses show that the proposed multiplexing architecture can achieve higher performance when the TDM ratio exceeds 67. The gain in performance of the proposed architecture over the existing architecture augments as the TDM ratio increases.