To establish chemical fingerprints of the aqueous extract and methanol extract of Cordyceps by HPLC. Methods:The aqueous extract and methanol extract of 20 batches Cordyceps and 2 batches Cordyceps mycelium were analyzed by HPLC. The chromatographic data was evaluated by similarity analysis and cluster analysis. Results:The aqueous extract and methanol extract chemical fingerprints of Cordyceps were developed. Seven common peaks were identified in aqueous extract and eight common peaks were identified in methanol extract. The similarities of 20 batches Cordyceps aqueous extract and methanol extract were higher than 0.9, and the similarities of 2 batches Cordyceps mycelium were lower than 0.9. The cluster analysis result showed that Cordyceps and Cordyceps mycelium were separated in different clusters. Conclusion:The developed HPLC fingerprint method is stable and reliable, which helps to the comprehensive quality evaluation of Cordyceps.