The fluctuation of sea surface and the Doppler effect cause carrier phase fluctuations of received signal, and the multipath expansion of the underwater acoustic channel makes received signal distorted, which can seriously influence the decoding performance of the cyclic shift spread spectrum system. In this paper, we propose cyclic shift energy detector (CS-ED) algorithm for cyclic shift keying spread spectrum system, which can solve the problem about the influence of carrier phase fluctuation by detecting the output energy of cyclic shift matched filter. The CS-ED combined with time reversal mirror is further proposed and analyzed in this paper by using a time-updated channel impulse-response estimate as a (match) filter to do time reversal processing to mitigate the multipath-induced interferences. Time reversal CS-ED method is simple and robust, which can make the system work in low SNR. Dalian Sea test validation and Lianhua lake test validation are carried on, showing that the low bit error rate underwater acoustic communication is achieved under the condition of multi-path extension, carrier phase fluctuation and low signal-to-noise ratio.