In the current era of biodiversity conservation, spatial zoning of protected areas plays a crucial role in safeguarding species and their habitats. Acknowledging the need to adapt these zones to the dynamic patterns of animal populations, we introduce a novel approach using Very High Resolution (VHR) remote sensing to identify individual whooper swans and analyze their population dynamics and distribution from 2009 to 2016, including an overwinter period, within a Chinese national nature reserve. Our analysis, juxtaposed with the reserve's current spatial zoning, informs recommendations for its adjustment. The results identify 1124 to 2190 birds across five images, with an average error of 4.65 ± 2.15%. Notably, the swan population on the wild western shores has tripled, while those in Yangyuchi Bay have plummeted from 20% to less than 2%. Mudflats, currently designated as buffer or experimental zones, and even unreserved areas, support over half of the swan population on average. We propose a rezoning of the reserve, suggesting the addition of 301.8 hectares to core zones. Our study demonstrates the effectiveness of wildlife remote sensing in the zoning and management of protected areas, enhancing the conservation of species like the whooper swan and contributing to the ambitious global target of conserving 30% of the Earth's land and sea areas by 2030.