According to the special operation conditions of low-head pumping stations with variable speed devices (VSD) in China’s South-to-North Water Diversion Project, the changing rules of pumping system performances under variable speed operation were investigated. It was pointed out that the conventional pump affinity laws were not suitable any more when the net head was greater than zero while VSD were used, and a new affinity law was proposed. By means of linearized pump performances at rated rotational speed, simplified methodologies predicting pumping system performances with VSD were put forward. After introducing the conception of specific energy, the energy consumptions of variable operation and other regulation methods were analyzed to pump a specific quantity of water within stipulated period. Based on the consideration of VSD efficiency, electric motor efficiency and the relationship of specific energy with the change of pump efficiency at different rotational speed, a method was brought forward to determine the reasonable and economic scope of variable speed under different net heads.