The region of the South China Sea is characterized by humid monsoon climate with frequent thunderstorms, which are dangerous weather phenomena. In this paper, we analyze a climatology of thunderstorms over the whole South China Sea using data from the WWLLN global thunderstorm localization network and analyzed the main statistical characteristics of thunderstorm activity for the ten years 2009–2018. A contribution to thunderstorm activity of 135 tropical cyclones passed over the South China Sea in this period is estimated. The climatological statistics are given for every month for each of 5 selected regions in the South China Sea. A high variability of the characteristics of thunderstorm activity as well as tropical cyclones in different areas of the sea is noted. When the highest contribution of tropical storms in the southern area occurs in winter months, it is maximum in summer and autumn in the northern regions. The averaged characteristics of thunderstorm activity in the South China Sea do not reflect all the details of its high spatial and temporal variability and connection with global, regional, and local features of atmospheric circulation and the morphology of adjacent land areas and islands, which will be done in the future studies.