The ecological protection red line is an important innovation in ecological conservation in China, and underpins a national policy for monitoring and managing important ecological environments. Guidelines for identifying the red line areas were issued by the Ministry of Environmental Protection of China in 2015. However, there are some technical difficulties in identifying the boundaries of the red line regions. This paper explores an optimization method to identify the ecological protection red line using the spatial analysis function of GIS software. Two initial principles are put forward: first, the boundary should be refined using higher resolution data when these boundaries are not within a nature reserve; second, the boundaries of the ecological protection red line should follow the boundaries of natural conservation areas. We applied the optimized method to identify the boundaries of the ecological protection red line using the Changping District of Beijing city as an example. The ecological functions of water conservation, soil conservation, sand fixation and biodiversity in the study area were identified and classified according to the rapid evaluation method on basis of net primary productivity (NPP) in the guidelines, and maps of their spatial distribution were produced. Then, spatial overlay analysis was carried out using the evaluation layers, and a comprehensive evaluation result was obtained by grading the evaluation output from the spatial overlay analysis. The preliminary design of ecological protection red line was established after removing some scattered small patches or merging the small patches into the adjacent large patches. Then, the preliminary design was optimized by overlaying a land use layer which had a higher spatial accuracy to identify the explicit boundary of the ecological protection red line region. The use of the high-accuracy land use layer transformed the low spatial resolution boundary to a high spatial resolution boundary after the overlay. Finally, the ecological protection red line was fine-tuned with reference to high resolution imagery and various planning policies. This fine-tuning will benefit the identification of much more accurate boundary locations for the ecological protection red line, and guarantee the implementation of the ecological protection policy in a specific land block with a clearly defined spatial extent. The above case study resolved the technical difficulties surrounding delineation of the ecological protection red line, and showed how to adjust and optimize the red line boundary. The feasibility of the research methods to solve the boundary definition problem was confirmed by comparing the ecological protection red line before and after adjustment.