Objective Considering the limitation of the one-sidedness and inaccuracy of the current network structure of cancer, a cancer-based network construction analysis assistant tool system based on integrated multiple data sources is given. Methods Based on the data source of cancer biological pathway of KEGG database and gene-disease relationship of DisGeNET database, the significantly differential pathways were obtained by using the pathway analysis method, and the network visualization tool was used to generate cancer network. The result was given by network clustering analysis. Results The genetic function of the clustering analysis and the biological function of the cluster network in cancer was analyzed. The result showed that the cancer network generated by the tool system and the network analysis result of clustering could accurately reflect the association between the cancer and the genes. Conclusions The system interface is friendly, human-computer interaction is good and also providing a novel way to construct a cancer network. The application shows that the result is good and can effectively assist the researchers. It is valuable and meaningful in the exploration to the pathogenesis of cancer.