Based on ultra-high performance liquid chromatography-triple quadrupole-tandem mass spectrometry (UPLCQQQ-MS/MS), a high throughput, sensitive and specific method to quantify three classes of phenolic compounds in tea samples was developed and validated. This method possessed good linearity, accuracy and precision, and was successfully applied to the simultaneous quantification of 90 phenolic compounds (catechins, phenolic acids, flavonoids and their glycosides) in four types of Yunnan large-leaf tea. As a result, most phenolic components were more abundant in unfermented tea (green tea and Pu’erh raw tea), while free phenolic acids, flavonoid aglycones and theaflavins were more abundant in fermented tea (black tea and Pu’erh ripe tea). By partial least squares-discriminant analysis (PLS-DA), different types of tea were clearly discriminated according to their phenolic components, and a series of chemical markers were identified.