Single-atom catalysts (SACs) have been investigated and applied to energy conversion devices. However, issues of metal agglomeration, low metal loading, and substrate stability have hindered realization of the SACs' full potential. Recently, covalent organic framework (COF)-based SACs have emerged as promising materials to enable highly efficient catalytic reactions. Here, we summarize the representative COF-based SACs and their wide application in clean energy devices and conversion reactions, such as hydrogen evolution reaction, carbon dioxide reduction reaction, nitrogen reduction reaction, oxygen reduction reaction, and oxygen evolution reaction. Based on their catalysis conditions, these reactions are categorized into photocatalyzed and electrocatalyzed reactions. We also summarize their design strategies, including heteroatom inclusion, donor-acceptor pairs, pore engineering, interface engineering, etc. Although COF-based SACs are promising, more efforts, such as linkage engineering, functional groups, ionization, multifunctional sites for cocatalyzed systems, etc., could improve them to be the ideal SAC materials. At the end, we provide our perspectives on where the field will proceed in the next 5 years.