[Objective] The cluster analysis was applied to the optimization of the Flavomycin flask fermentation. [Methods] The data of Flavomycin flask fermentation from different batches was clustered by using system cluster, K-means cluster and fuzzy C-means cluster. The result showed that fuzzy C-means cluster was better than the other two. [Results] Then the classes were separated and the excellent samples were distilled, moreover, the range of control parameter of Flavomycin flask fermentation was optimized. [Conclusion] The experiment results indicated that cluster analysis was effective in the optimization of fermentation process.