Using time-dependent 3D tomography method, the electron density distributions in the low-latitude ionosphere during November 2004 super-storm are reconstructed from GPS observations of joint ground-based IGS network and onboard CHAMP/GRACE satellites. The reconstructed electron densities are validated by satellite in situ measurements of CHAMP and GRACE satellites. It is indicated by computer tomography (CT) reconstructions that the long-lived positive storm phase during the first main phase of the storm (November 8) is mainly attributed to enhancement of electron density in the upper F region above the F2 peak. It is found by the CT imaging that the top-hat-like F2-3 double layers occurred in the equatorial ionization anomaly region during the main phase of the storm (at forenoon of November 8). The structures of column-like enhanced electron density are found at the time near the minimum of Dst and in the longitudinal sector about 157°E, which extend from the topside ionosphere toward plasmasphere, reaching at least about 2000 km as high. Their footprints stand on the two peaks of the EIA.