•Dynamic model predicts ecosystem tipping points under exploitation, revealing surprising biodiversity impacts and guiding conservation efforts.

Ecosystems are undergoing unprecedented persistent deterioration due to unsustainable anthropogenic human activities, such as overfishing and deforestation, and the effects of such damage on ecological stability are uncertain. Despite recent advances in experimental and theoretical studies on regime shifts and tipping points, theoretical tools for understanding the extinction chain, which is the sequence of species extinctions resulting from overexploitation, are still lacking, especially for large-scale nonlinear networked systems. In this study, we developed a mathematical tool to predict regime shifts and extinction chains in ecosystems under multiple exploitation situations and verified it in 26 real-world mutualistic networks of various sizes and densities. We discovered five phases during the exploitation process: safe, partial extinction, bistable, tristable, and collapse, which enabled the optimal design of restoration strategies for degraded or collapsed systems. We validated our approach using a 20-year dataset from an eelgrass restoration project. Counterintuitively, we also found a specific region in the diagram spanning exploitation rates and competition intensities, where exploiting more species helps increase biodiversity. Our computational tool provides insights into harvesting, fishing, exploitation, or deforestation plans while conserving or restoring the biodiversity of mutualistic ecosystems.