Deep understanding of the fluorescence quenching mechanisms of probes plays a crucial role in developing their practical applications. The fluorescence quenching mechanism of hydrazine‐based fluorescence probes needs to be clarified up to the present. Herein, we designed and synthesized a new hydrazine‐based fluorescence probe (HA‐Na) based on the naphthalimide skeleton. We clarified the molecular origin of the non‐fluorescence of this probe with the aid of computational chemistry and spectroscopic analysis. We showed that the significant rotation of the hydrazine group in the excited state potential energy surface, which caused the complete charge separation, was responsible for the fluorescence quenching of the probe in an organic solvent. Once the rotation was prevented in an aggregative state or high‐viscosity solution, the fluorescence of the probe recovered. In other words, the fluorescence quenching mechanism of hydrazine‐based fluorescence probes was attributed to the formation of a twisted intramolecular charge transfer (TICT) state. More importantly, we demonstrated that this fluorescence molecular rotor could be used to monitor the autophagy process in living cells by detecting lysosomal viscosity changes during starvation. Altogether, this work provides an essential theoretical basis for the developing potential hydrazine‐based fluorescence molecular rotors.