AbstractSpread spectrum technology has been widely employed for positioning and communicating with autonomous underwater vehicles (AUVs), but conventional spread spectrum sequences lack confidentiality and reliability in UWA channel. Considering the limitations of conventional sequences and the characteristics of underwater acoustic (UWA) channel, a composite chaotic orthogonal sequence (CCOS) based on the UWA channel is proposed. The confidentiality of the CCOS is superior to that of the m‐sequence, while the autocorrelation performance of the CCOS is superior to that of the orthogonal sequence. Moreover, the CCOS can compensate for the imbalance of logistic chaotic sequence when assigned certain initial values. Acquisition is a crucial component of accessing the spread spectrum signal; therefore, the acquisition performance indicates the applicability of the CCOS. The source–target model is established to simulate communication with an underwater moving target. To simulate the acquisition process, a parallel algorithm based on fast Fourier transform is adopted, and the entire simulation process is completed based on the BELLHOP ray acoustic model. Through data processing, the Doppler shift error is less than half of the frequency‐search element. Furthermore, the acquisition probabilities of the CCOS with different numbers of bits are over 90%, which demonstrates the reliability of the CCOS.