The invention discloses a red fluorescent protein-based two-photon photosensitizing dye RFP-Ac and a preparation method and application thereof. The red fluorescent protein-based two-photon photosensitizing dye RFP-Ac comprises phenothiazine, vinylbenzene and fluorescent protein methylene The conjugated structure of the base imidazolidinone, and the aryl acrylate was introduced at the end group of the fluorescent chromophore as an active thiol recognition site and a photosensitizer targeting group. The red fluorescent protein-based photosensitizing dye molecule RFP-Ac of the present invention has two-photon absorption characteristics, a Stokes shift of more than 200 nm, strong anti-interference ability, high sensitivity, low cytotoxicity, good biocompatibility, and singlet oxygen production. It can be used as two-photon photosensitizing dyes and fluorescent probes with high performance in near-infrared wavelengths for fluorescence sensing, endogenous or exogenous bioactive thiol detection, two-photon fluorescence imaging, fluorescent labeling, two-photon light Dynamic therapy has a wide range of applications.