In mountain rivers with coarse sediments, the ratio of water depth to sediment diameter (h/d) is relatively small especially under the condition of shallow water depth. Therefore, the vertical velocity distribution along the river cannot be described accurately with traditional logarithmic or logarithmic-wake law. In this paper, flume experiments were carried out with two kinds of sediments (glass beads d=1.4 cm and pinpong d=4 cm) to test the influence of coarse sediment on vertical velocity distribution under different h/d. In the presence of coarse sediment bed, one of the problems encountered is how to determine the reference level y0. For practical purpose, the present study assumes that y0 does not varies with h/d, namely, y0=0.2d. The measured data were first converted to dimensionless and then compared to theoretical results calculated by logarithmic-wake law. In addition, the coefficient B and another wake coefficient Π in in logarithmic compensation formula were calibrated to fit for the measured data. The results indicate that when the value of h/d is small, the coefficient B decreases with the increase of h/d while the wake coefficient Π presents an opposite trend, when the value of h/d becomes larger, both B and Π tend to a constant. Finally, a modified logarithmic-wake law is derived to describe the velocity distribution in mountain river flows with small h/d. The modified model agrees well with the experimental data conducted in the present laboratory flume. Furthermore, it also has a good adaptability to riverbed with coarse sediments.