A method for processing an automatic identification system (AIS) baseband signal based on a field-programmable gate array (FPGA) is provided. A signal output by a bus is cached in a message buffer and then sent to a Gaussian filtered minimum shift keying (GMSK) modulator after being encoded by a frame encoder. Another signal output by the bus is processed by an AIS access control module and then also sent to the GMSK modulator. The two signals output by the bus are respectively output to two digital to analog converters (DACs) after being modulated by the GMSK modulator; a digital signal is converted into an analog signal, and the analog signal is sent to an I/Q or two-point modulation radio frequency (RF) circuit. Two received baseband signals are respectively input into analog to digital converters (ADCs) and separately sent to the bus.