The invention discloses an FPGA-based multipath HDLC-UART conversion system and method. The system adopts hardware description language to realize conversion of multipath HDLC communication protocols and UART communication protocols based on an FPGA, and a data frame calibration control function. The system comprises an UART data frame acquisition and unpacking module, an UART-data-frame-to-HDLC-data-frame check processing module, an HDLC data frame coding output module, an HDLC data frame acquisition and unpacking module, an HDLC-data-frame-to-UART-data-frame check processing module, an UART data frame coding output module, an UART data frame cut-through forwarding module, an UART control command response module, a forwarding mode control module and an HDLC clock control module and the like. Through construction of multiple groups of the modules above based on the FPGA, a multipath HDLC-UART communication protocol conversion controller is realized, and parameters in the conversion controller are configured flexibly, system design flexibility and design efficiency are improved and the system has a good practical application value.