In this study, a three-dimensional (3-D) ionospheric tomography was developed in Japan using the constraint least-square fitting algorithm, a model-free method. Moreover, to make enough room for electron density (Ne) variations in the horizontal direction, only constraints on height were adopted. Slant total electron content data sets detected by 800 Global Positioning System (GPS) ground-based receivers in 25°–50°N, 125°–150°E were selected. The spatial resolution was 1°, 1°, and 30 km in latitude, longitude, and altitude, respectively. The reconstructed performances concerning the quiet ionosphere, large-scale traveling ionospheric disturbances on July 27, 2004, and nighttime medium-scale traveling ionospheric disturbances on June 23, 2012, were verified successively. By comparing with Ne distributions from the International Reference Ionosphere model and GPS-TEC mapping, the reconstructed results in both horizontal and vertical directions show good performance in imaging the ionospheric background and disturbed characteristics. The finding strongly indicates that retrieving Ne distributions by the improved constraint least-square algorithm is promising for ionospheric studies and practical applications.