The IUCN Red List has downgraded several species from “endangered” to “vulnerable” that still have largely unknown extinction risks. We consider one of those downgraded species, the giant panda, a bamboo specialist. Massive bamboo flowering could be a natural disaster for giant pandas. Using scenario analysis, we explored possible impacts of the next bamboo flowering in the Qinling and Minshan Mountains that are home to most giant pandas. Our results showed that the Qinling Mountains could experience large-scale bamboo flowering leading to a high risk of widespread food shortages for the giant pandas by 2020. The Minshan Mountains could similarly experience a large-scale bamboo flowering with a high risk for giant pandas between 2020 and 2030 without suitable alternative habitat in the surrounding areas. These scenarios highlight thus-far unforeseen dangers of conserving giant pandas in a fragmented habitat. We recommend advance measures to protect giant panda from severe population crashes when flowering happens. This study also suggests the need to anticipate and manage long-term risks to other downgraded species.