To address current ecological issues and a lack of historical preservation in Beijing’s waterfront, it has become necessary to establish an urban design project that optimizes these aspects. This study focuses on “Beijing’s Waterfront Overall Urban Design,” a project that integrates government requirements with Beijing’s waterfront urban design characteristics and problems to establish an urban layer system from two dimensions: historical and ecological. It explores how the urban layer system can be applied to Beijing’s overall waterfront urban design, from investigation to evaluation, analysis, visualization, and strategy development. First, an urban layer system for Beijing’s waterfront was established from a historical perspective, based on urban setting and construction stages and space utilization, referring to the literature and field surveys. The evolution of urban layers of waterbodies, the water–city relationship, and water functions was systematically analyzed. Second, an urban layer system was established for the ecological dimension of Beijing’s waterfront based on a literature review, expert interviews, and analytic hierarchy process methods. It included four urban layers: waterbody, greening, shoreline, and ecological function. The quality of the ecological urban design of 54 waterfront reaches in Beijing was evaluated using questionnaires and field surveys. Third, a series of urban layer maps was generated using the mapping method. Finally, urban design strategies were developed based on the combined historical and ecological characteristics and problems of Beijing’s waterfront. The results of this study and the concept of an urban layer system for waterfront urban design can benefit waterfront urban design projects and future studies.