The main proteases (Mpros) are hydrolases playing essential roles in the replication of β-coronaviruses including SARS-CoV-2. Herein, a highly efficient strategy was developed for discovering the Mpro inactivators from crude plant extract integrating target-based biochemical assay and chemoproteomic approaches. Firstly, Pu-erh tea was found to potently suppress SARS-CoV-2 Mpro in a time-dependent manner. Next, global chemical analysis coupling with peptide-modification profiling were used to identify the cysteine-modified constituents in Pu-erh tea. The results suggested that seven constituents in Pu-erh tea could modify SARS-CoV-2 Mpro, which turned out that epigallocatechin, gallocatechin and gallic acid were the most efficacious Mpro inactivators. Further investigations demonstrated that epigallocatechin and gallocatechin could inactivate SARS-CoV-2 Mpro via blocking the formation of the homodimers. Collectively, this work proposed a novel and practical strategy for highly efficient discovery of time-dependent inhibitors of SARS-CoV-2 Mpro from plant extracts, while 3 constituents in Pu-erh tea have emerged as robust SARS-CoV-2 Mpro inactivators.