Large scale ion density structures were observed by ROCSAT-1 at 630 km altitude over the South Atlantic anomaly (SAA) region during the great magnetic storm of July 15-16, 2000. The observed density structures were confined within 30° in longitude east of the SAA, and co-rotated with the SAA for over 8 hours. The magnetic anomaly density structures (MADS) observed during several successive orbits in the nighttime sector, contained density holes and density pile-ups adjacent to each other. The density holes had a density drop of one to two orders of magnitude below the ambient level and a spatial size of 800 - 1800 km along the satellite path. The density pile-ups typically spanned a spatial size of 2000 ~ 3000 km were characterized with a density enhancement, large density fluctuations and upward drift velocity. In contrast to density pile-ups, density holes did not exhibit noticeable density fluctuations nor upward drift velocity. A common feature of large poleward drifts was noticeable inside both density hole and pile-up structures. The ion drift measurements thus indicate that ions inside the density holes drifted away in the poleward direction rather than the upward direction. The successive observations of density holes on six orbits suggest that the density hole might be initially created near the center of SAA region and then expanded equatorward. We interpret the magnetic anomaly density pile-up to be the ionospheric F2 peak layer raised to the satellite altitude by storm enhanced eastward electric fields. It is speculated that energetic particle precipitation might have occurred in the region of magnetic anomaly density structures, increasing locally ionospheric conductivity in the E region and producing eastward polarization electric fields in the precipitation region. The combination of localized polarization electric fields and storm time electric fields at low latitudes in the nightside might be responsible for the ion drifts and the associated anomalous density structures observed by ROCSAT-1 in the F region.