In underwater acoustic channels, multipath propagation and Doppler frequency can distort the received signal and reduce system reliability. In order to effectively combat multipath interference, the Sweep-Spread Carrier (SSC) system using frequency swept signal is proposed, however, the SSC receiver performs well only when the maximum delay spread of path arrivals and the Doppler spread are moderate. In this paper, fractional Fourier transform (FrFT) is applied to channel equalization of the SSC system, which improves the ability to resist the Doppler effect and intersymbol interference (ISI). FrFT can simplify the channel characteristics by selecting an appropriate transform order. We analyze the FrFT equalizer in the SSC system under the zero forcing (ZF) criterion and minimum mean squared error (MMSE) criterion. Compared with typical nonlinear Turbo equalization, FrFT equalizer only requires lower complexity to achieve good performance. The numerical simulation results in bellhop and ray tracing channels and the results of the Wu-yuan Bay test channel show the high robustness of the proposed method in doubly dispersive channels.