AbstractLong‐term variations of South Atlantic anomaly (SAA) are generally derived by fitting a Gaussian‐like function to an averaged distribution of the proton flux at a certain altitude accumulated over time periods for a month or longer. These data do not show the short‐term variation of SAA arising from geomagnetic storm effects whose time scale is less than a month. To investigate the short‐term variations, the features of SAA for the high‐energy protons detected by NOAA Polar Orbiting Environmental Satellites during 1998–2008 have been investigated with a 5 day running average method. It is found that the two SAA parameters for three proton channels reflect the maximal proton flux in SAA and the extension of SAA decreases several percent during geomagnetic storms. Possible reasons for the decreases of the two SAA parameters for high‐energy protons are discussed. Proton losses at the outer boundary of the inner radiation belt can be explained by the field line curvature scattering mechanism, while the decrease of the proton flux near the center of SAA is probably caused by the enhanced neutral atmospheric density during geomagnetic storms. The study of the behavior of high‐energy protons in SAA is useful for understanding of storm time and long‐term variations of the radiation environment near Earth and for constructing dynamic radiation belt models.