Based on the basic principle and method of BP neural network, this paper built the water security evaluation model of BP neural network of double hidden layers. The evaluation model was verified by relevant literature. The results shows that the evaluation model and method of double hidden layer BP is reasonable and feasible and is a regional water security evaluation method witch can be used. Based on this model, combined with the situation of wet areas, the paper set up a water safety evaluation index system and standard by using analytic hierarchy process, and evaluated the water security by taking Wenshan for example. The results show that water safety evaluation grade at each evaluation region of Wenshan in different level years is Ⅱ-Ⅳ, which is between unsafe and safe and reflects the objective situation and medium and long-term water security condition of the area,and is consistent with regional actual, evaluation results can be used as regional water security evaluation reference for research area.