Transcription factors c-Jun and Fra-1 have been reported to play a role during the initiation and progression in oral squamous cell carcinoma (OSCC). However, cohort studies are rarely reported. Here is an integrative analysis of their prognostic value in OSCC through a multicenter cohort study.313 OSCC patients were included in this study and received regular follow-up. The survival rate and hazard ratios( HR) were generated by survival analysis. The concordance probability and receiver operating characteristic curve area were chosen to measure the model discrimination. High expressions of c-Jun or Fra-1 were associated with poor prognosis, meanwhile the high expression of Fra-1 meant worse prognosis of patients than the high expression of c-Jun. Besides, the interaction effect of c-Jun and Fra-1 was antagonism, when the expression of c-Jun and Fra-1 was both high, the HR was lower than the hazard ratio when only the Fra-1 was at high expression. c-Jun and Fra-1 were both proved to be high risky predictors of death in OSCC, the antagonistic effect suggested that these biomarkers’ activities could be influenced by each other. It may provide a new sight for the studies of OSCC prognosis and treatment.