Riboswitches are highly conserved RNA elements capable of recognizing small molecule ligands and modulating downstream gene expression. To date, nearly 60 types of riboswitches have been identified, each recognizing different metabolites and small molecules. With the increasing discovery of riboswitches, their sequence features, tertiary structures, and regulatory mechanisms become focal points of research. Tertiary structure-based studies provide invaluable insights into understanding the ligand recognition and downstream gene expression mechanisms of riboswitches. In this review, we provide an overview of the diversity and primary functions of known riboswitches, with a specific focus on the tertiary structures and ligand recognition mechanisms of cofactor riboswitches. Additionally, we discuss the applications and future prospects of riboswitches.