To investigate the reasons for the flowrate deviation of the prototype pumping systems between the measured value onsite and the calculated one by the similarity law, the energy characteristic relationship of the prototype and model pumping systems under different working conditions was compared and analyzed. It was pointed out that the hydraulic loss in the outlet passages caused by the residual velocity circulation is not similar. Using the method of vessel-mounted ADCP and water level gauges to measure the flowrates and heads of pumping stations, the energy characteristics of three typical pumping stations were obtained, and the comparisons with the characteristic curves of the pumping systems predicted by similarity law are made. It was found that there was a deviation between the two in most cases, and the similarity deviation of the elbow inlet and siphon outlet passages was greater than that of the straight pipe inlet and outlet passages. Meanwhile that the larger the blade angle (or the higher the rotational speed of pump), the greater the similarity deviation. Therefore, in the design of the pumping system, the energy characteristics of the model pumping system cannot be simply converted by the similarity law to predict the characteristics of the prototype pumping system, but the influence of different factors on the similarity deviation between the prototype and model pumping system should be considered carefully.