Multipath propagation, frequency selective fading, low-propagation velocity, and narrow bandwidth are all characteristics of underwater acoustic channels. Doppler shifts and diffusions can occur as a result of the low transmission speed of an acoustic signal, which can be caused by the movement of ocean currents or the transceiver. Furthermore, frequency selective fading and excessive noise interference can disrupt underwater acoustic communication on a continual basis. Because of its high anti-interference ability and high confidentiality, spread spectrum technology is commonly adopted in underwater acoustic communications. Although the direct sequence spread spectrum method has a low data rate, it is advantageous in a multipath propagation channel environment or an environment with a low signal-to-noise ratio (SNR). This advantage is suitable for long-distance transmission or LPD (Low Probability of Detection) communication, and the direct sequence spread spectrum method is applied. In this paper, we propose a highly reliable M-ary cyclic spread spectrum technique by superimposing the M-ary spread spectrum, an extension of the direct sequence spread spectrum technique, and cyclic shift keying. Furthermore, by estimating the Doppler frequency using M-ary spread spectrum codes and performing synchronization correction of the ensuing symbol based on the estimation results, higher performance can be attained. Simulations and experiments showed that the M-ary cyclic spread spectrum method can reduce Doppler estimation and synchronization error accumulation while maintaining a high data rate. Furthermore, the MCSS method had a lower bit error rate than the standard spread spectrum method.