Fluorophores and fluorophores‐based probes or labels can visualize the structures and content fluctuations of biomolecules, and have made great progress in the broad range of biomedicine fields. However, many commercially available fluorophores suffer from small Stokes shift, which results in insufficient signal‐to‐noise ratio and self‐quenching in advanced imaging techniques. Moreover, the small Stokes shift also hinders the application of fluorophores in some complex imaging, such as single‐excitation multicolor imaging. In the past two decades, many effects have been made to enlarge Stokes shift of fluorophores. In this review, we clarified the reasons for the small Stokes shift building on the structural analysis of fluorophores, systematically summarize the methods of structural modification to increase Stokes shift, and present some representative applications of fluorophores with large Stokes shift in imaging and sensing.