The emergence and prevalence of metallo-β-lactamases (MβLs)-mediated bacterial resistance has seriously threatened the global health today. MβLs are deemed to be one of the most worrying bacterial resistance factors that hydrolyze nearly all β-lactam antibiotics. However, none of MβL inhibitors have appeared in clinic to date. This review surveys the common covalent targets in B1 and B2 MβLs, summarizes all covalent inhibitors of MβLs and their inhibition modes as of 2020, highlights the importance of the rational design of covalent MβL inhibitor guided by the crystal structure and the development of dual-action covalent MβL/SβL inhibitors based on lysine residue of MβLs and serine residue of SβLs, and describes the approaches to discern the covalent inhibition mechanism to guide the development of future therapeutics.