Biodiversity and climate are interconnected through carbon. Drivers of climate change and biodiversity loss interact in complex ways to produce outcomes that may be synergistic, and biodiversity loss and climate change reinforce each other. Prioritizing the conservation of flagship and umbrella species is often used as a surrogate strategy for broader conservation goals, but it is unclear whether these efforts truly benefit biodiversity and carbon stocks. Conservation of the giant panda offers a paradigm to test these assumptions. Here, using the benchmark estimates of ecosystem carbon stocks and species richness, we investigated the relationships among the giant panda, biodiversity, and carbon stocks and assessed the implications of giant panda conservation for biodiversity and carbon-focused conservation efforts. We found that giant panda density and species richness were significantly positively correlated, while no correlation was found between giant panda density and soil carbon or total carbon density. The established nature reserves protect 26 % of the giant panda conservation region, but these areas contain <21 % of the ranges of other species and <21 % of total carbon stocks. More seriously, giant panda habitats are still facing high risks of habitat fragmentation. Habitat fragmentation is negatively correlated with giant panda density, species richness, and total carbon density. The ongoing giant panda habitat fragmentation is likely to cause an additional 12.24 Tg C of carbon emissions over 30 years. Thus, giant panda-focused conservation efforts have effectively prevented giant panda extinction but have been less effective in maintaining biodiversity and highcarbon ecosystems. It is urgent for China to contribute to the development of an effective and representative national park system that integrates climate change issues into national biodiversity strategies and vice versa in dealing with the dual environmental challenges of biodiversity loss and climate change under a post-2020 framework.