The loss of biodiversity is irreversible and represents one of humanity’s greatest sustainability challenges. It has severe consequences for ecosystems and human well-being and requires global action. China, a global biodiversity hotspot, has experienced rapid habitat loss due to land-use change. Yet, current assessments, such as the IUCN Red List, suffer from incomplete coverage and fail to account for dynamic changes in habitat. This creates critical gaps in conservation planning. Here, we integrate species composition dissimilarities with satellite-derived land-use changes to quantify extinction risks across China. Our findings reveal a nationwide increase in extinction risk (3.91%) alongside a decline in habitat (2.81%). Current protected areas disproportionately prioritize lower-risk western regions, while IUCN assessments often overlook high-risk areas in human-modified landscapes. Our results establish a framework for quantifying extinction risks driven by dynamic habitat loss—a critical dimension that traditional IUCN metrics neglect. We provide actionable insights to advance sustainable development goals.