The invention discloses an FPGA remote online debugging method, device and system based on optical fiber communication. The method comprises the steps of: S1, building an FPGA remote online debuggingsystem based on optical fiber communication, wherein the system comprises an antenna housing provided with an interface conversion circuit, an interface converter, and a debugging computer; the antenna housing provided with the interface conversion circuit is connected with the interface converter through an optical fiber, and the interface converter is connected with the debugging computer. The invention provides an effective means for remote debugging of a secondary radar system, solves the problems of long-distance transmission of online debugging signals and easy interference of the signals in the working period of a secondary radar, solves the problem that the number of signal channels of a mechanical scanning radar rotating joint is limited, solves the problem that the personal safety of maintenance personnel cannot be guaranteed in the maintenance period, debugging / maintenance work can be carried out anytime and anywhere, and safety, high efficiency, simplicity, convenience andthe like are realized.