The field of network security is highly concerned with intrusion detection, which safeguards the security of computer networks. The invention and application of intrusion detection technology play indispensable roles in network security, and it is crucial to investigate and comprehend this topic. Recently, with the continuous occurrence of intrusion incidents in virus propagation networks, traditional network detection algorithms for virus propagation have encountered limitations and have struggled to detect these incidents effectively and accurately. Therefore, updating the intrusion detection algorithm of the virus-spreading network is imperative. This paper introduces a novel system for virus propagation, whose core is a graph-based neural network. By organically combining two modules—a standardization module and a computation module—this system forms a powerful GNN model. The standardization module uses two methods, while the calculation module uses three methods. Through permutation and combination, we obtain six GNN models with different characteristics. To verify their performance, we conducted experiments on the selected datasets. The experimental results show that the proposed algorithm has excellent capabilities, high accuracy, reasonable complexity, and excellent stability in the intrusion detection of virus-spreading networks, making the network more secure and reliable.