Aiming at the problem that synchronized correlation of linear frequency synchronization of m sequence possesses self noise and there are strong side lobes in a code range besides main lobe, in this paper we propose a new underwater acoustic synchronization scheme based on binary offset carrier (BOC) modulated signal with no interference windows which employs the property that the sum of aperiodic auto correlation function is 0 to realize no interference window between the range of one code and zero inference window and utilizes BOC (1, 1) to modulate signal with sub-carrier to mitigate side lobes in one code range besides main lobe. The schemes are designed for both single and couple channel signal, and the validity of underwater acoustic synchronization, channel measurement and estimation are testified through simulation and experiments.