Weighted fractional Fourier transform-based hybrid carrier communication can be regarded as a combination of single-carrier communication and multicarrier communication, providing strong flexibility due to the changeable transform order. The hybrid carrier underwater acoustic communication based on the joint time-frequency domain equalization is proposed in this paper. With the time-domain equalization based on time reversal, multipath spreads of underwater acoustic channels can be greatly suppressed. Thus, the length of the required cycle prefix is shortened, improving the bandwidth efficiency. The residual intersymbol interference can be removed using frequency-domain equalization based on the minimum mean square error or zero force. The experimental results show that the optimal transform orders to achieve the best communication performance are different in different environments. Compared with the traditional frequency-domain equalization method, the proposed method performs better with respect to bit error rate and bandwidth efficiency. INDEX TERMS Weighted fractional Fourier transform, hybrid carrier, time reversal mirror, frequency domain equalization, cycle prefix.