In recent years, China’s resource and environmental problems have become increasingly severe, and the pressure on resource constraints has continued to increase. The Chinese government has delineated constraints for spatial planning based on the ecosystem, that is, a “red line for ecological protection”, which aims to “control the ecological space” and optimize the ecological environment. The optimized verification of this red line can improve the accuracy of its boundary, ensure habitat integrity, and provide data and methods supporting the protection of the ecosystem. In this study, the problems of verifying the boundary of the ecological protection red line include five major categories and 24 minor categories, such as accuracy problems, current situation problems, contradictions with planning, boundary consistency problems, and integrity problems. Taking Fangshan District, Beijing, China, as an example, based on the results of delineating the ecological protection red line in Fangshan District, we integrated geographical monitoring, land use surveys, high-resolution remote sensing images, small forestry classes, protected areas, road networks, water networks, and 14 types of multi-source data, such as architectural and planning data. On the basis of the idea of clustering, we granulated the types of plaques in the ecological protection red line into three categories, nature reserves, river wetlands, and other protection units, and we assessed multi-source data regarding the specific problems of various types of plaques in the ecological protection red line. We used an adaptive design, using the big data processing mode of red line plaque fragmentation, based on ArcGIS spatial data analysis and processing functions to optimize and verify the red line boundary. We obtained a mapping accuracy of 1:10000 for the ecological protection red line, which is a breakthrough in accuracy. This study provides a base map for ecological protection via the red line management, supervision, and comprehensive implementation of land and space planning. The research method is also applicable to research on optimizing the red line boundary for ecological protection in other regions of the country.