In essence, the network is a way of encoding the information of the underlying social management system. Ubiquitous social management systems rarely exist alone and have dynamic complexity. For complex social management systems, it is difficult to extract and represent multi-angle features of data only by using non-negative matrix factorization. Existing deep NMF models integrating multi-layer information struggle to explain the results obtained after mid-layer NMF. In this paper, NMF is introduced into the multi-layer NMF structure, and the feature representation of the input data is realized by using the complex hierarchical structure. By adding regularization constraints for each layer, the essential features of the data are obtained by characterizing the feature transformation layer-by-layer. Furthermore, the deep autoencoder and NMF are fused to construct the multi-layer NMF model MSDA-NMF that integrates the deep autoencoder. Through multiple data sets such as HEP-TH, OAG and HEP-TH, Pol blog, Orkut and Livejournal, compared with 8 popular NMF models, the Micro index of the better model increased by 1.83, NMI value increased by 12%, and link prediction performance improved by 13%. Furthermore, the robustness of the proposed model is verified.