A prototype verification system and method are provided for a high-end fault-tolerant computer. The system includes multiple single junction prototype verification systems and an interconnection router chipset. The single junction prototype verification systems are interconnected through the interconnection router chipset. Each single junction prototype verification system includes a computer board which is a four-path tightly-coupled computer board, and a chip verification board including two junction controller chipsets. Each junction controller chipset includes two field-programmable gate array (FGPA) chips which bear a logic of one junction controller together, and an interconnection board including two FGPA chips. Each FPGA chip provides a high speed interconnection port used to achieve protocol interconnection between two paths of the computer board and one of the junction controller chipsets.