The invention discloses a transform domain underwater acoustic communication method based on chaotic spread spectrum, and the method comprises the following steps: S1, carrying out sampling of an environment channel at a transmitting end and a receiving end, obtaining an environment noise signal, and carrying out the FrFT processing of the environment noise signal, and obtaining an environment spectrum vector; S2, obtaining a double-chaotic sequence through an improved Logistic mapping structure, processing the double-chaotic sequence, and obtaining a pseudo-random phase through FrFT; S3, after the environment spectrum vector is matched with the pseudo-random phase, carrying out amplitude adjustment to obtain an FrFT domain basis function, and carrying out IFrFT on the FrFT domain basis function to obtain a time domain basis function; S4, performing baseband mapping on the time domain basis function of the transmitting end at the transmitting end to obtain a spread spectrum signal, and sending the spread spectrum signal to a receiving end; and S5, performing related demodulation on the spread spectrum signal at a receiving end through a time domain conjugate basis function of thereceiving end to obtain an information signal. The method has better concealment, anti-interference capability, anti-multipath capability and the like, and can realize reliable communication under a very low signal-to-noise ratio.