Extranodal NK/T-cell lymphoma nasal type (ENKTL) is a subtype of T cell lymphoma with poor prognosis. In this study, we designed a new prognostic model specifically for ENKTL to improve the risk stratification. In 29 ENKTL patients, we screened mutations in 9 ENKTL-associated genes using next-generation sequencing (NGS). We have found that mutated KMT2D was associated with the inferior overall survival (OS) and progression free survival (PFS) and KMT2D or TP53 mutations were associated with a higher mortality rate. Moreover, the difference in PFS among different stratifications was not significant using the International Prognostic Index (IPI) alone but was significant after the mutation status of KMT2D and TP53 were incorporated into the IPI model, forming a harmonious risk stratification reflecting the clinical features and genetic information of ENKTL. In summary, we demonstrate that the prognostic value of the IPI system can be enhanced by integrating the status of genetic mutations.