Cyanine dyes have been widely used in phototherapy in recent years due to their excellent optical properties and diverse modifiable structures. This review provides detailed descriptions of the basic structures of various cyanines and their derivatives as well as their optical properties. It summarizes the strategies for constructing cyanine dyes for phototherapy and discusses their structure-effect relationship. Furthermore, a comprehensive classification and summary of the applications of cyanine dyes in phototherapy are presented. Importantly, this review also addresses both the advances made in this field as well as the challenges that need to be overcome. We hope that these profound insights into phototherapy using cyanine dyes will facilitate the design of future systems for clinical applications based on these compounds.