Common seasonal variations in Global Positioning System (GPS) coordinate time series always exist, and the modeling and correction of the seasonal signals are helpful for many geodetic studies using GPS observations. A spatiotemporal model was proposed to model the common seasonal variations in vertical GPS coordinate time series, based on independent component analysis and varying coefficient regression method. In the model, independent component analysis (ICA) is used to separate the common seasonal signals in the vertical GPS coordinate time series. Considering that the periodic signals in GPS coordinate time series change with time, a varying coefficient regression method is used to fit the separated independent components. The spatiotemporal model was then used to fit the vertical GPS coordinate time series of 262 global International GPS Service for Geodynamics (IGS) GPS sites. The results show that compared with least squares regression, the varying coefficient method can achieve a more reliable fitting result for the seasonal variation of the separated independent components. The proposed method can accurately model the common seasonal variations in the vertical GPS coordinate time series, with an average root mean square (RMS) reduction of 41.6% after the model correction.