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Despite numerous global initiatives and policy framework to mitigate ongoing biodiversity decline, progress remains limited due to lack of biodiversity indicators that are timely, scientifically rigorous, and representative. Furthermore, databases underlying previous indicators are spatially, temporally, geographically and taxonomically biased, making it difficult to track biodiversity change dynamics and set proper biodiversity targets. Here, we constructed a new version of the global human footprint, and used it to infer temporally explicit annual shifting patterns of biodiversity across all scales by incorporating remote sensing and mapping out human pressures. This indicator (the Ecological Integrity Index- EII) successfully differentiates high- and low- biodiversity biomes, especially for deserts and tundra. Moreover, shifting annual patterns can identify global hotspots (e.g., major rainforests and regional hotspots), and shows biodiversity change dynamics at regional level based on estimating biodiversity change over time. Changes of evolving human footprint were further analyzed with relationships to biodiversity patterns. At more a local level, the patterns perfectly reflect biodiversity and intactness. Compared to other indicators (e.g., BII, BHI) in the Kunming-Montreal Global Biodiversity Framework (GBF) and biodiversity models (e.g., GLOBIO), the EII can better reflect biodiversity. EII shows a good performance, with the potential to inform biodiversity conservation efforts, and support the implementation of the post-2020 global biodiversity framework.