Rapidly developing droughts, including flash droughts, have occurred frequently in recent years, causing significant damage to agroforestry ecosystems, and they are expected to increase in the future due to global warming. The artificial forest area in China is the largest in the world, and its carbon budget is crucial to the global carbon sink. As the most prominent plantation plant in the tropics, the rubber (Hevea brasiliensis (Willd. ex A. Juss.) Muell. Arg.) ecosystem not only has important economic significance, but also has the potential to be a major natural carbon sink in hot areas. Frequent drought events have a significant impact on rubber ecosystem productivity, yet there have been few reports on the vulnerability of rubber productivity to drought. The objective of this study is to evaluate the vulnerability of rubber ecosystem gross primary production (GPP) to short-term flash drought (STFD) in Hainan Island, utilizing the localized EC-LUE model (eddy covariance–light use efficiency) validated by flux tower observations as the research tool to conduct the scenario simulations which defined by standard relative humidity index (SRHI), in a total of 96 scenarios (timing × intensity). The results show that, in terms of time, the rubber ecosystem in Hainan Island has the highest vulnerability to STFD during the early rainy season and the lowest at the end of the rainy season. From the dry season to the rainy season, the impact of STFD gradually extends to the northeast. Spatially, the vulnerability of the northern island is higher than that of the southern island and that of the western part is higher than that of eastern Hainan Island. With the increase in STFD intensity, the spatial distribution center of the vulnerability of rubber ecosystem GPP in Hainan Island gradually moves southward. The spatiotemporal pattern of the vulnerability of the rubber ecosystem GPP to STFD over Hainan Island plotted by this study is expected to provide decision makers with more accurate information on the prevention and control of drought disaster risk in rubber ecosystems.