Excited-state intramolecular proton-transfer (ESIPT) based fluorescence probes are particularly attractive due to their unique properties including environmental sensitivity, a large Stokes shift, and potential for ratiometric sensing. In general, ESIPT-based fluorophore incorporates an intramolecular hydrogen bonding interaction between a hydrogen bond donor (–OH and NH2 are common) and a hydrogen bond acceptor (C=N and C=O). More, protection–deprotection of hydroxyl group as hydrogen bond donor could induce an off-on switch of ESIPT-based emission. Therefore, protection–deprotection of hydroxyl group has been the widely used strategy to design fluorescent probes, where the potential key issue is selecting a protective group that can specifically leave in the presence of the target analyte. In this review, we mainly summarize the specific protecting groups (sites) and deprotection mechanisms for biologically important species (including reactive sulfur species (RSS), reactive oxygen species (ROS), enzymes, etc.), and analyze the advantages and disadvantages of different protection mechanisms from some aspects including probe stability, selectivity, response rate and assay system, etc. Based on the aforementioned, we further point out the current challenges and the potential future direction for developing ESIPT-based probes.