With the continuous development of network security situations, the types of attacks increase sharply, but can be divided into symmetric attacks and asymmetric attacks. Symmetric attacks such as phishing and DDoS attacks exploit fixed patterns, resulting in system crashes and data breaches that cause losses to businesses. Asymmetric attacks such as Advanced Persistent Threat (APT), a highly sophisticated and organized form of cyber attack, because of its concealment and complexity, realize data theft through long-term latency and pose a greater threat to organization security. In addition, there are challenges in the processing of missing data, especially in the application of symmetric and asymmetric data filling, the former is simple but not flexible, and the latter is complex and more suitable for highly complex attack scenarios. Since asymmetric attack research is particularly important, this paper proposes a method that combines causal discovery with graph autoencoder to solve missing data, classify potentially malicious nodes, and reveal causal relationships. The core is to use graphic autoencoders to learn the underlying causal structure of APT attacks, with a special focus on the complex causal relationships in asymmetric attacks. This causal knowledge is then applied to enhance the robustness of the model by compensating for data gaps. In the final phase, it also reveals causality, predicts and classifies potential APT attack nodes, and provides a comprehensive framework that not only predicts potential threats, but also provides insight into the logical sequence of the attacker’s actions.