According to the comparative analysis of the differences between data measured by three-point method and five-point method used in the Yangtze River Flood Control prototype and model, and those data measured by verticall-average flow velocity method adopted in the physical model, the deviation degrees of prototype-model flow velocities along water depth are compared. The authors discuss the law of velocity distribution along the vertical direction after model metamorphosis using the Nullah-Logarithmic velocity equation, and, on the basis of this analysis, propose the relations between the average vertical velocity and the relative location of the depth. Observation data analysis show that velocity of the 0.6 relative water depth is basically consistent with the average vertical velocity.