The amplitudes of seasonal signal in GNSS coordinate time series shows obvious time-varying characteristics. In this paper, the vertical coordinate time series of 468 GNSS stations around the world are selected to deeply explore the time-varying characteristics and cause of annual amplitudes. First, after band-pass filtered, the time series are fitted by piecewise least squares to get the time-varying amplitudes of the annual signal. Then, the magnitude and characteristics of amplitude variation are analyzed. It is found that the average magnitude of annual amplitude changes is about 1 mm. Moreover, the fluctuation of amplitude has obvious temporal and spatial distribution characteristics. Ignoring this time-varying characteristic will lead to a maximum annual residue of 2 similar to 3 mm. Then, we deeply investigate the contributions of the environmental loading and thermal expansion effects to the annual amplitude changes. The result shows it is about 60% that the average consistency of amplitude changes between the GNSS vertical coordinates and displacement caused by environmental loading and thermal expansion, and that after the two corrections, about 68% and 76% of the stations have a decrease in the annual amplitude fluctuation respectively. It is suggested that the environmental loading and thermal expansion effects are the important reasons for the amplitude variation of the annual signal. Meanwhile, we find that the GNSS data processing model and strategy will also cause the change of annual amplitudes.