To ensure the reliability and safety of expressway networking systems, this paper designs a data flow risk monitoring system for expressway networking systems based on deep learning. The monitoring system is composed of data flow risk analysis, formulation of safety strategy, real-time monitoring, and disaster recovery. Data flow risk analysis is the basis for the operation of each part of the system. Meanwhile, indexes such as network management, data assets, and network resources are selected to build a data flow risk monitoring index system. The deep convolution neural network model is constructed, and the data flow risk monitoring index data are input into the deep convolution neural network to extract the index data features through the convolution and pooling process.Based on this, feature mapping is realized with a multilayer perceptron, and the index data risk classification results of data flow risk monitoring are output by the SoftMax classifier. The experimental resultsshow that the monitoring system can obtain accurate data flow risk analysis results which effectively reduces the data loss rate, alleviate the impact of different types of malicious attacks, and ensure the stability and security of the experimental object.