Continuous improvement of internet technology has driven the continuous progress and improvement of industrial control systems, and provided more support for security vulnerability detection in this field. Combining the GAN model, the detection model based on Seq-GAN in industrial control protocol vulnerabilities constructed in this article provides more options for further improving the security of industrial control systems, and can detect and analyse security vulnerabilities in industrial control protocols more efficiently and accurately. By comparing the performance of different models for security vulnerability detection, the Seq-GAN model has smaller prediction errors, can also obtain higher G-mean and F1-score values, and has sufficient reliability. At the same time, it can also improve the efficiency of vulnerability detection in industrial control systems, and can achieve better comprehensive detection performance. Therefore, the application of the Seq-GAN model in industrial control protocol vulnerability detection can provide more support for improving security detection in this field.