Cities are a hotspot for biodiversity and an important spatial component of ecological civilization and sustainable development. The importance of biodiversity conservation has been mentioned many times in previous studies in landscape architecture and urban and rural planning. Still, specific conservation measures and policies have been studied generally, which is not conducive to the full implementation of urban biodiversity conservation. This study focuses on the hotspots of biodiversity-friendly green space planning and is based on an in-depth case study approach. Taking Japan as a representative country, this study analyses the policies related to biodiversity-oriented urban green space master plans; taking the Shinjuku district in Japan as the core case, it analyses the method of constructing ecological networks within the central area of the city and clarifies the specific process of biodiversity conservation policies from planning to implementation; summarizes the experience of the three-step process of “pre-survey-mid-planning-post-implementation” in the planning of biodiversity-friendly green space systems. The three-step experience of “pre-survey-mid-planning-post-implementation” in the planning of biodiversity-friendly green space systems is summarized. Its applicability to the relevant fields in China is discussed considering the actual practice of green space planning in China. The corresponding experience is sorted out to provide a reference for future urban biodiversity conservation work and ecological civilization construction in China at the level of planning, control, and implementation, as well as theoretical methods.