Due to the complexity of the social network server system, various system abnormalities may occur and in turn will lead to subsequent system failures and information losses. Thus, to monitor the system state and detect the system abnormalities are of great importance. As the system log contains valuable information and records the system operating status and users’ behaviors, log data in system abnormality detection and diagnosis can ensure system availability and reliability. This paper discloses a log analysis method based on deep learning for an intrusion detection system, which includes the following steps: preprocess the acquired logs of different types in the target system; perform log analysis on the preprocessed logs using a clustering-based method; then, encode the parsed log events into digital feature vectors; use LSTM-based neural network and log collect-based clustering methods to learn the encoded logs to form warning information; lastly, trace the source of the warning information to the corresponding component to determine the point of intrusion. The paper finally implements the proposed intrusion detection method in the server system, thereby improving the system’s security status.