In view of high dimension, big data, the difficulty of getting labeled samples, the problem of feature expression and training existed in the application of neural network in intrusion detection, an intrusion detection method based on Multiple Layer Extreme Learning Machine (ML-ELM) was proposed in this paper. Firstly, the highest level abstract features of the detection samples were extracted by multi-layer network structure and deep learning method. The characteristics of intrusion detection data were expressed by singular values. Secondly, the Extreme Learning Machine (ELM) was used to establish the classification model of intrusion detection data. Then, the problem that hard to obtain labeled samples was solved by using a layer by layer unsupervised learning method. Finally, the KDD 99 dataset was used to test the performance of ML-ELM. The experimental results show that the proposed model can improve the detection accuracy, and the false negative rate of detection is low to 0.48%. The detection speed can be improved by more than 6 times compared with other depth detection methods. What's more, the detection accuracy is still more than 85% in the case of a few labeled samples. The detection rates of U2L attack and R2L attack are improved by constructing multi-layer network structure. The method integrates the advantages of deep learning and unsupervised learning. It can express these features of high dimension and large data well using fewer parameters. It also has a good performance in intrusion detection rate and characteristic expression.