Wuyi Rock Tea is a kind of semi-fermented oolong tea, with unique flavor. The alkaloid content in the tea is associated with its flavor quality. In this study, 10 typical Wuyi Rock Tea, including 5 Rougui and 5 Shuixian, were used to quantitative analyze the theobromine, theophylline and caffeine content in the tea leaves and tea infusions. Moverover, the alkaloid content in green tea, Tieguanyin Tea and black tea sample were also measured. Then, Principal Component Analysis (PCA) was utilized to further investigate the difference of the alkaloid content in all these tea samples. The results indicated that, the caffeine, theobromine and theophylline content in the Wuyi Rock Tea leaves were 2.341%, 0.065% and 0.011%, respectively, which were lower than those ingreen tea, Tieguanyin Tea and black tea. After immersed in boiling water for 60 s, approximate 46.56%, 46.36% and 50.15%of caffeine, theobromine, and theophylline were dissolved into the infusions. PCA analysis shown that Wuyi Rock Tea samples had significantly different alkaloid profile with green tea, Tieguanyin Tea and black tea.