Pre-warning system of water resources security is a multi-level and complex system made of many factors. By analyzing current situation of water resources security pre-warning, operating mechanism of water resources security pre-warning system is put forward, Logic, time and knowledge related to operating mechanism are discussed. For pre-warning threshold decision is one of key technology in water resources security pre-warning, warning threshold decision and warning degree classification of water resources security pre-warning are set forth. These methods are systematic method, control chart method, synthetic judgement method, catastrophism method and expert decision method. Adopting the water resources security pre-warning system, situation can be analyzed and predicted promptly and effectively.