The Earth’s ionosphere can be described by a spherical harmonic (SH) expansion up to a specific degree. However, there exist negative vertical total electron content (VTEC) values in the global ionosphere map (GIM) with the SH expansion model. In this contribution, we specifically investigated the negative VTEC values that are induced by the SH expansion model and validated the performance of the inequality-constrained least squares (ICLS) method in eliminating the negative VTEC values. The GPS data from 2004 to 2017 was selected to cover one solar cycle and the experiments under different solar activity conditions were analyzed. The results in our work show that the occurrence of the negative VTEC values is attributed to the deficiency of the SH expansion model when the VTEC itself is small instead of the unevenly distribution of the GNSS stations. The negative VTEC values appear periodically in the temporal domain, showing apparently one year and half year periods. During one year, two peaks in June and December can be observed in the time series of the negative VTEC values. The number of negative VTEC values in June is obvious larger than that in December. During one solar cycle, the number of negative VTEC values under quiet solar activity condition is obvious larger than that under strong solar activity condition. In the spatial domain, the appearance of the negative VTEC values is strongly related with the movement of the subsolar point. In the latitude of the subsolar point has the largest magnitude, the negative values will appear on the opposite hemisphere and the further from the subsolar point the more negative values. The maximum number of the negative VTEC values in the southern hemisphere appears in June, while the peak value in the northern hemisphere appears in December. The maximum number of negative VTEC values in the southern hemisphere is generally larger than that in the northern hemisphere. In addition, the negative VTEC values are distributed both at middle latitude and high latitude in the southern hemisphere, while they are mainly distributed at high latitude in the northern hemisphere. When the ICLS method is used, the negative VTEC values can be eliminated efficiently and it has nearly no influence on the positive VTEC values. The ICLS method can also improve the receiver’s differential code bias (DCB) and significantly decrease the unreasonable negative slant TEC (STEC) values along the lines of sight. Using the final GIM product of the Jet Propulsion Laboratory (JPLG) as a reference, the root mean square (RMS) of the ICLS solution shows maximum 25%, 20% and 45% improvement relative to the least squares (LS) solution at northern high latitude, southern middle latitude and southern high latitude, respectively.