Thermophilic cyanobacteria are prokaryotic organisms that possess exceptional heat-resistant characteristics. This group serves as an excellent model for investigating the heat tolerance of higher photosynthetic organisms, including higher plants, some protists (such as algae and euglena), and bacteria. Analyzing the mechanisms of high-temperature adaptation in thermophilic cyanobacteria can enhance our understanding of how photosynthetic organisms and microorganisms tolerate high temperatures at the molecular level. Additionally, these thermotolerant cyanobacteria have the potential to contribute to breeding heat-tolerant plants and developing microbial cell factories. This review summarizes current research on thermophilic cyanobacteria, focusing on their ecology, morphology, omics studies, and mechanisms of high-temperature tolerance. It offers insight into the potential biotechnological applications of thermophilic cyanobacteria and highlights future research opportunities. Specifically, attention is given to the photosynthetic physiology and metabolism of cyanobacteria, and the molecular basis of heat-tolerance mechanisms in thermophilic cyanobacteria is explored.