A multi-protocol serial interface system comprises a multi-protocol port pin array, a transport protocol change FPGA, a pull-up change FPGA and a memory. The multi-protocol port pin array comprises a plurality of port pins which interface with an external system for exchanging data with the external system. The transport protocol change FPGA determines roles of port pins of the multi-protocol port pin array depending on a variably changed protocol by selecting one of the plurality of programmed transport protocol circuits in response to code data. The pull-up change FPGA regulates pull-up load of the port pins corresponding to the roles of the port pins determined in the transport protocol change FPGA. The memory stores data processed in the transport protocol change FPGA unit and exchanged with the external system.