Enhancing ecological security for sustainable social, economic, and environmental development is a key focus of current research and a practical necessity for ecological management. However, the integration of retrospective ecological security assessments with future trend predictions and fine-scale targeted regulations remains inadequate, limiting effective ecological governance and sustainable regional development. Guided by Social–Economic–Natural Complex Ecosystems (SENCE) theory, this study proposes an analytical framework that integrates ecological security assessment, prediction, and zoning management. The Daqing River Basin, a typical river basin in the North China Plain, was selected as a case study. The results indicate that overall ecological security in the Daqing River Basin improved from a “Moderate” level to a “Relatively Safe” level between 2000 and 2020; however, spatial heterogeneity persisted, with higher ecological security in northwestern and eastern regions and lower ecological security in the central region. Approximately 62% of the Basin experienced an improvement in ecological security level, except in the major urban areas of Beijing, Tianjin, and Hebei, where ecological security deteriorated. From 2025 to 2040, the overall ecological security of the Daqing River Basin is expected to improve and remain at the “Relatively Safe” level. However, spatial heterogeneity will be further aggravated as the ecological security of major urban areas continues to deteriorate. Ecological security management zones and regulation strategies are proposed at the regional and county scales to emphasize integrated regulation for the entire basin and major urban areas. The proposed analytical framework provides valuable insights for advancing theoretical research on ecological security. The case study offers a practical reference for ecological security enhancement in river basins and other regions facing significant human–land conflicts.