Extreme events caused by global change are increasingly affecting the ocean’s biogeochemical cycling and ecosystem functioning, but it is challenging to observe how food webs respond to rapid habitat disturbances. Benthic communities are particularly vulnerable because their habitats are easily affected by extreme events. Here, we examined how benthic macrofauna responded to a “near shutdown” of shallow marine hydrothermal vents, triggered by M5.8 earthquake and C5 typhoon events. Despite reduced vent fluxes, we shows that the endemic vent crab Xenograpsus testudinatus continued to rely on chemosynthetic sulfur bacteria rather than photosynthetic sources. We posit this obligate nutritional dependence caused a population decline of vent crabs. In contrast, the non-endemic mollusks exhibited much greater dietary plasticity with no detectable impact on the population. Our study based on naturally occurring extreme events exemplifies how specialist species in marine system are particularly vulnerable to the unprecedented evolutionary and environmental pressures exerted by human activities worldwide.