SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the etiological agent responsible for the global COVID-19 (coronavirus disease 2019) outbreak. The main protease of SARS-CoV-2, M, is a key enzyme that plays a pivotal role in mediating viral replication and transcription. We designed and synthesized two lead compounds ( and ) targeting M Both exhibited excellent inhibitory activity and potent anti-SARS-CoV-2 infection activity. The x-ray crystal structures of SARS-CoV-2 M in complex with or , both determined at a resolution of 1.5 angstroms, showed that the aldehyde groups of and are covalently bound to cysteine 145 of M Both compounds showed good pharmacokinetic properties in vivo, and also exhibited low toxicity, which suggests that these compounds are promising drug candidates.