AbstractThe South Atlantic Anomaly (SAA) refers to a region where the strength of the magnetic field is notably weaker compared to a dipole field. While previous studies have primarily focused on its effects on the inner radiation belt, this study investigates its impact on the aurora system. By analyzing 2 years' worth of data obtained by the Fengyun‐3E/ACMag instrument, we discover that magnetic fluctuations within the auroral oval are significantly weaker in the longitude sector corresponding to the SAA, as compared to those outside this area. This characteristic remains permanent and independent of seasons and geomagnetic activities. Additional investigation using Defense Meteorological Satellite Program/Special Sensor Ultraviolet Spectrographic Imager (DMSP/SSUSI) observations reveals a similar phenomenon in the auroral intensity. Therefore, our results demonstrate that the SAA substantially weakens the aurora system, shedding new light on the effects of magnetic anomalies on planetary auroras and magnetosphere‐ionosphere‐thermosphere coupling.