Abstract: In the broadband acoustic Doppler current profiler (BBADCP), the Doppler shifts of the echoes reflected from different water layers are calculated by using pseudo-random coded modulation and complex correlation algorithm to achieve the purpose of velocity measurement. It is known that in the complex correlation algorithm, there is a direct proportional relationship between the accuracy of velocity measurement and the length of pulse signal when the disturbance of ambiguous velocity is eliminated. However, for increasing pulse length, the higher coding order would be used to modulate the transmitting pulse signal, which brings the problem of velocity ambiguity. Based on the complex correlation frequency measurement algorithm and aiming at the periodic frequency measurement ambiguity of long-coded pulse signal, in this paper, a method by using the frequency measurement result of short-coded pulse signal as the discrimination criterion and choosing the appropriate periodic frequency offset as the calculation result is proposed, which can not only improve the velocity measurement accuracy, but also solve the problem of periodic velocity ambiguity while increasing precision. In practical application, the velocity measurement accuracy of this method is improved under low signal-to-noise ratio.