The invention discloses a high-reliability underwater acoustic communication synchronization signal detection method and system. The high-reliability underwater acoustic communication synchronizationsignal detection method comprises the following steps: firstly, the ambient noise is estimated, and a detection threshold value is confirmed according to a set detection threshold; then the copy correlation detection is performed on a received signal to judge whether the amplitude of the received signal exceeds the detection threshold value or not; if not exceeded, the received signal is discarded; and if exceeded, the fractional order Fourier transform domain search is performed on the copy of the received signal to estimate the frequency modulation slope, and whether the detected received signal is a synchronization signal or not is judged according to the error between the frequency modulation slope and the true value. The invention uses the time-frequency joint analysis characteristicof the fractional order Fourier transform to perform secondary detection on false alarm signals, and reduces the influence of the false alarm signals on the underwater acoustic communication system, which has the characteristics of simple realization and high reliability.