The impacts of intense tourism development and inappropriate recreation utilization are increasingly apparent in ecotourism. The sustainable development of ecotourism is faced with severe challenge. From the perspective of a total relationship flow management, this paper explores recreation impacts in ecotourism and clarifies the determinants in ecotourism system behaviour. Based on the total relationship flow management theory, the paper analyzes the structure and hierarchy within the ecotourism system, and further proposes a management framework for recreation impacts in ecotourism areas. The results reveal a series of inherent relationships and their laws among various ecotourism system behaviors, functions and its total relationship flow, and remedy the methodological deficiencies in reductionism and holism research. In the paper, Danxia Mountain is adopted as a case study to explore the applicability of recreation impacts management framework in practices. The study provides a theoretical foundation and a scientific management model in examining recreation impacts of ecotourism areas, which is expected to help managers gain new insights and improve their performances in managing ecotourism areas.