The invention discloses a frequency domain chirp spread spectrum based hydroacoustic communication system and communication method. A sending end comprises a channel coding unit, a frequency domain chirp mapping unit, a subcarrier mapping unit, an inverse fast Fourier transform unit, a cyclic prefix adding unit and a windowing unit. A receiving end comprises a time synchronization unit, a carrier wave synchronization unit, a cyclic prefix removing unit, a multipath frequency mixing filtering unit, a chirp correlation demodulation unit, a channel decoding unit and a frequency tracking unit. Channel coding, frequency domain chirp mapping and subcarrier mapping are performed on input data at the sending end, and through inverse fast Fourier transform, cyclic prefix adding and windowing, signals are sent to a hydroacoustic channel; and a time synchronization, carrier synchronization and frequency tracking process is performed on receiving signals at a receiving end, cyclic prefixes are removed, frequency mixing filtering is performed on the receiving signals respectively with the central frequency of each piece of frequency domain chirp data so as to obtain signals after the multipath frequency mixing filtering, then chirp correlation demodulation is performed respectively with time domain up-chirp signals and time domain down-chirp signals, a result is determined, and through channel decoding, reduced data is output.