The invention discloses a gate pump joint control-based water filling method for a water transfer project of an open channel of a cascade pump station, and relates to the technical field of water filling of the water transfer project. According to the water filling method, by adopting a gate pump joint control technology, a water pump quickly meets a startup condition, quick water filling of the project is realized, water filling time and water loss in a water filling stage are shortened and reduced, and water filling efficiency is improved; meanwhile, by getting water from a water source fullof water resources, the water filling efficiency is remarkably improved, and the water resource waste and the water loss of a system are reduced; and in addition, through flap gate control, the channel water surface curve of the water filling process is reduced, and the channel water filling safety is ensured.