The real-time control of the schedule of each work is one of the main tasks of schedule management of water conservancy project groups. While, how to use economic bonus and penalty to effectively control the schedule of each work is the key to their schedule management. The sub-network of the water conservancy project groups is formulated according to the influence scope and degree induced by the schedule delay of various work items. On this basis, emphasis is laid on the influence mechanism of various work items of water conservancy project groups on the schedule of the contract project, sub-networks of the project groups and the project groups. The corresponding economic penalty model is established. The penalty amounts of each work and each contract project are then determined. Finally, a case study is carried out to illustrate the application mechanism and method of the economic penalty model. The economic penalty model for the schedule delay of water conservancy project groups based on the work can provide the basis for the scientific and reasonable determination of the penalty amount of each work and each contract project, and also lay the foundation for the employer to determine the key contract projects and work items of the schedule control in the water conservancy project groups.