Gravity waves (GWs) generated in the lower atmosphere can propagate upwards to ionospheric height. In this study, we investigated the correlation between ionospheric GWs detected by Global Navigation Satellite System (GNSS)-derived total electron content data and thunderstorm events recorded by a local lightning-detection network in the low-latitude region of Southern China during a four-year period, from 2014 to 2017. Ionospheric GWs were detected on both thunderstorm and non-thunderstorm days. Daytime ionospheric GW activity on high-thunderstorm days showed a similar convex-function-like diurnal variation to thunderstorm activity, which is different to the concave-function-like pattern on non-thunderstorm days. Daytime ionospheric GW activity on low-thunderstorm days showed an approximately linear rising trend and was of a larger magnitude than that of high-thunderstorm days, suggesting it may be mixed by non-thunderstorm origins. Night-time enhancement of ionospheric GW activity was observed on thunderstorm days but not on non-thunderstorm days. Furthermore, ionospheric GW activity on thunderstorm days showed a positive correlation to solar activity. These findings can effectively distinguish thunderstorm-related ionospheric GWs from those of non-thunderstorm origins and provide more comprehensive knowledge of thunderstorm-ionosphere coupling in low-latitude areas.