Relativistic electron precipitation (REP) from the Earth’s radiation belt plays an important role in mesospheric ozone loss as a connection between space weather and the climate system. However, the rapid (tens of minutes) destruction of mesospheric ozone directly caused by REP has remained poorly understood due to the difficulty of recognizing its location and duration. Here we show a compelling rapid correspondence between localized REP and ozone destruction during a specific auroral phenomenon, the called an isolated proton aurora (IPA). The IPA from the Earth’s radiation belt becomes an important spatial and temporal proxy of REP, distinct from other auroral phenomena, and allowing visualizing micro-ozone holes. We found ozone destruction of as much as 10–60% within 1.5 h of the initiation of IPA. Electromagnetic ion cyclotron waves in the oxygen ion band observed as the driver of REP likely affect through resonance with mainly ultra-relativistic (> 2 mega-electron-volts) energy electrons. The rapid REP impact demonstrates its crucial role and direct effect on regulating the atmospheric chemical balance.