The reaction of a series of electron‐deficient isoindolium‐based allenes with sulfhydryl compounds has been studied, leading to the formation of isoindolium‐based vinyl sulfides. The vinyl sulfides generated could be readily converted into the corresponding indanones and amines upon heating at 30–70 °C with good yields up to 61 %. The thermal cleavage reaction of vinyl sulfides was further studied for developing temperature‐sensitive systems. Notably, a novel FRET‐based fluorescent temperature sensor was designed and synthesized for temperature sensing at 50 °C, giving a 6.5‐fold blue fluorescence enhancement. Moreover, chemoselective bioconjugation of cysteine‐containing peptides with the isoindolium‐based allenes for the construction of multifunctional peptide bioconjugates was investigated. Thermal cleavage of isoindoliums on the modified peptides at 35–70 °C gave indanone bioconjugates with up to >99 % conversion. These results indicated the biocompatibility of this novel temperature‐sensitive reaction.