The water security of Shule River Basin has an important impact on the ecological security of Qilian Mountains. Aiming at the water security problem of Shule River Basin, an environment-ecology- supervision-governance model was proposed to construct a water safety evaluation index system for the inland river basin in Qilian Mountains. The index data was processed using fuzzy C-means (FCM) algorithm combined with expert scoring method, and then the water security of the Shule River Basin was evaluated using learning vector quantization(LVQ) network model. The results were compared with those of the models using LVQ neural network only and BP neural network only to verify the applicability of the proposed model. The results show that the water security status of the Shule River Basin was evaluated as “unsafe” in 2013, “quasi-safe” from 2014 to 2016, and “safe” from 2017 to 2019, which presented a gradual upward trend. This is consistent with the actual situation in the basin. In addition, the FCM-LVQ network model is obviously superior to the other two network models in terms of running speed and accuracy of evaluation results, so it is recommended for watershed water security evaluation.