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Along with habitat destruction and the intensification of climate change, economic and social development is threatening the living of species. In the context of China's domestic economic circulation, the spatial structure of biodiversity loss is complicated by the decentralization of production, with many regions affecting the survival of species in other regions. Based on the environmentally extended MRIO model, this paper calculated the subnational biodiversity loss footprint through structural path analysis and social network analysis, identified the regional linkages and spatial networks of species loss, and traced the conservation responsibility to specific sectors. Our findings indicate that Yunnan, Tibet, Guangdong, and Sichuan possess the most significant biodiversity footprints, comprising over 40% of the total footprint. In terms of threat patterns, Yunnan and Tibet have the largest intra-regional footprints, indicating their important impact on species within the region; Guangdong and Zhejiang have the largest extra-regional footprints, indicating their role in threatening other species through cross-regional trades. The primary industry, tap water and food and tobacco sectors are major biodiversity footprint producers. Overall, some eastern and coastal areas are the final drivers of biodiversity loss in China, driven by increasingly complex trade links. Notably, the directionality of species loss in biodiversity hotspots is evident, with Shandong and Guangdong significantly influencing the biodiversity of Yunnan and Guangxi, respectively. This study systematically analyzed the complete network of biodiversity loss and divided four biodiversity protection communities to promote the realization of trans-regional protection and compensation. Examining the biodiversity loss through the lens of networks, and connecting economic activities to species, serves as a warning to decision-making bodies that a future of increasingly intricate domestic trade could pose a critical threat to biodiversity, necessitating collaborative conservation efforts. [Display omitted] • 1.Inter-provincial trade contributes to the complex structure of biodiversity loss. • The characteristics of biodiversity footprints vary widely among provinces. • Some eastern and coastal provinces are the final drivers of biodiversity loss. • Four protection communities are established through social network analysis. [ABSTRACT FROM AUTHOR]