The invention relates to a ship automatic identification system with an RF agile transceiver AD9361. The system comprises an antenna, a limiter, a low noise amplifier, a band-pass filter, a transformer, an AD9361, an ARM, an FPGA, a CPCI and a power supply. In the ship automatic identification system, a radio frequency signal is input into a digital signal output and a digital signal is input into a radio frequency signal output through the AD9361 by virtue of receiving channels of two different frequency points and a transmitting channel, and a single-ended signal can be converted into a differential signal only by a transformer before entering a chip, and signal transmission can be implemented by the device as long as a corresponding digital signal is input and a transformer for converting differential signals to single-ended signals is additionally arranged. The ship automatic identification method has the beneficial effects that the circuit area is reduced, the circuit performance is improved, and excellent isolation and noise coefficients can be realized.