Next-generation sequencing (NGS) genomic data offer valuable high-throughput genomic information for computational applications in medicine. Using genomic data to identify disease-associated genes to estimate cancer mortality risk remains challenging regarding to computational efficiency and risk integration. For determining mortality-related genes, we propose an information fusion system based on a fuzzy system to fuse the numerous deep-learning-based risk scores, consider the significance of features related to time-varying effects and risk stratifications, and interpret the directional relationship and interaction between outcome and predictors. Fuzzy rules were implemented to integrate the considerations mentioned above by merging all the risk score models to achieve advanced risk estimation. The genomic data of head and neck squamous cell carcinoma (HNSCC) were used to evaluate the performance of the proposed computational approach. The results indicated that the proposed computational approach exhibited optimal ability to identify mortality risk-related genes in HNSCC patients. The results also suggest that HNSCC mortality is associated with cancer inflammatory response, the interleukin-17A signaling pathway, stellate cell activation, and the extracellular-regulated protein kinase five signaling pathway, which might offer new therapeutic targets HNSCC through immunologic or antiangiogenic mechanisms. The proposed information fusion system can promote the determination of high-risk genes related to cancer mortality. This study contributes a valid cancer mortality risk estimate that can identify mortality-related genes.