Abstract: In order to further reveal the flow characteristics over dunes and thus improve the calculation accuracy of velocity, the time-mean velocity profile was analyzed both experimentally and theoretically, and the instantaneous velocities were measured over two different forms of dunes at a shallow depth by virtue of Acoustic Doppler Velocimeter (ADV). Based on the secondary flow formula proposed by Yue, together with the flow characteristics of dunes, a formula of velocity vertical distribution over dunes, including the functions of development and correction, was put forward on the premise that the secondary flow on the stoss side was a continuous evolution process. The results showed that the effects of dunes on incident flow surface became more significant with the decrease of relative depth of water, which made the upside velocity decrease and near-bed velocity increase. By comparison with flume experimental data, the proposed formula had a good agreement with measured values, which could well describe the velocity profile.