Traditional water-soluble organic macrocyclic receptors generally lack photofunctionality, thus monitoring the drug delivery and the phototheranostic applications of these host-guest macrocyclic systems has been greatly restricted. To address this issue, incorporating π-conjugated dye chromophores as building blocks into macrocyclic molecules is a straightforward and promising strategy. This approach not only imparts intrinsic optical features to the macrocycles themselves but also enhances the host-guest binding ability due to the large planar structures of the dyes. In this feature article, we focus on recent advances in water-soluble macrocyclic compounds based on organic dye chromophores, such as naphthalimide (NDI), perylene diimides (PDI), azobenzene (azo), tetraphenylethylene (TPE) and anthracene, and provide an overview of their various applications including molecular recognition, drug release, biological imaging, photothermal therapy, etc. We hope that this article could be helpful and instructive for the design of water-soluble dye-based macrocycles and the further development of their biomedical applications, particularly in combination with drug therapy and phototheranostics.