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There are a large number of excellent research cases in Global Navigation Satellite System (GNSS) positioning and disaster prediction in Japan region, where the simulation and prediction of total electron content (TEC) is a powerful research method. In this study, we used the data of the GNSS Earth Observation Network (GEONET) established by the Geographical Survey Institute of Japan (GSI) to compare the performance of two regional ionospheric models in Japan, in which the spherical cap harmonic (SCH) model has the best performance. In this paper, we investigated the spatial and temporal variations of ionospheric TEC in Japan and their relationship with latitude, longitude, seasons, and solar activity. The results show that the TEC in Japan increases as the latitude decreases, with the highest average TEC in spring and summer and the lowest in winter, and has a strong correlation with solar activity. In addition, the observation and analysis of ionospheric disturbances over Japan before the 2016 Kumamoto earthquake and geomagnetic storms showed that GNSS observing of ionospheric TEC seems to be very effective in forecasting natural disasters and monitoring space weather. [ABSTRACT FROM AUTHOR]