Cyanine dyes, one of the most important classes of organic fluorophores, have recently attracted more and more attention for their applications in fluorescence imaging, tumor phototheranostics, and fluorescence imaging-guided tumor surgery. Wavelength, photostability, and fluorescence brightness are three key factors determining the performance of cyanine dyes. However, the photostability of cyanine dyes requires improvement, and the emission wavelengths of some cyanine dyes are relatively short, which limits their biological applications. Significantly, cyanine dyes, with excellent biocompatibility, good fluorescence brightness, high molar extinction coefficient, and tunable absorption/fluorescence wavelength, exhibit a great prospect in cancer phototheranostics. In this review, the recent research progress of molecular engineering strategies of cyanine dyes is summarized, the general synthesis methods of cyanine fluorophores are briefly introduced, and their applications of cyanine dyes in fluorescence imaging and phototherapy are highlighted.