Abstract: Research on space genes, which reveals the spatial organization laws of urban form, plays a crucial role in balancing ecological protection, cultural inheritance, and contemporary development, offering significant value for both research and practice. However, due to the absence of a systematic approach to identifying space genes, the objectivity, completeness, and reliability of findings are often questionable. Based on an in-depth understanding of space genes, this study proposes that the key to identifying space genes lies in the recognition of interactions between space, nature, and humans within urban characteristic spaces. The identification process is elaborated in five steps: summarizing urban characteristic spaces; gaining public recognition of characteristic spaces; clustering and filtering of spatial cognition features; abstracting the configuration relationships of spatial elements; and integrating a set of spatial organization rules. Accurately identifying space genes directly enhance the operational efficiency and accuracy of space gene analysis and its practical applications. This approach contributes effectively to planning and design for local sustainable development.