High-risk neuroblastoma is a very aggressive disease, with excessive tumor growth and poor outcomes. A proper stratification of the high-risk patients by prognostic outcome is important for treatment. However, there is still a lack of survival stratification for the high-risk neuroblastoma. To fill the gap, we adopt a deep learning algorithm, Autoencoder, to integrate multi-omics data, and combine it with K-means clustering to identify two subtypes with significant survival differences. By comparing the Autoencoder with PCA, iCluster, and DGscore about the classification based on multi-omics data integration, Autoencoder-based classification outperforms the alternative approaches. Furthermore, we also validated the classification in two independent datasets by training machine-learning classification models, and confirmed its robustness. Functional analysis revealed that MYCN amplification was more frequently occurred in the ultra-high-risk subtype, in accordance with the overexpression of MYC/MYCN targets in this subtype. In summary, prognostic subtypes identified by deep learning-based multiomics integration could not only improve our understanding of molecular mechanism, but also help the clinicians make decisions.