The invention discloses an intelligent draining scheduling system and method. The system comprises a daily energy-saving submodule and an emergency scheduling submodel. The system is based on a pump station model and a pipe network model. The daily energy-saving submodule solves a minimum energy consumption solution of a pipe network through employing a genetic algorithm, and can effectively solve a problem that the daily energy consumption of a pump station is too high. The emergency scheduling submodel enables each pump station to give play to the strongest draining capability of the pipe network for draining during scheduling at each time, and can effectively solve a problem that the pipe network cannot give play to the strongest draining capability.