In fractional Fourier domain (FrFD) hopping communication, a chirp signal distinguishes others only when their center frequency and/or frequency rate difference is significant, which is not easy to realize in the band-limited underwater acoustic (UWA) channels. Hence suppressing nonoptimal order chirps in FrFD is required to facilitate the detection of UWA FrFD hopping (FrFDH) communication. In the context of UWA communication, a FrFDH scheme based on multi-frequency-rate chirp modulation is proposed, therein fractional Fourier transform (FrFT) incorporates the independent component analysis (ICA) algorithm for mitigating the inter-domain interference (IDI) and increasing the input signal-noise ratio of input signal at the receiver. Results from simulation and field test indicate that the chirps in different domains can be separated from each other, and better performance is achieved compared with the conventional scheme.