Abstract: The article integrates the principles of ‘base pairing’ and ‘DNA sequence combination’ of biological genetic genes, systematically constructs a research method of five scales which is geographical regions, settlement systems, settlement units, building groups, and building units, and two systems of ‘morphological genes’ and ‘cultural genes’ to ‘multi-scale’ identify and ‘dual system’ interpret the landscape genes of traditional settlements, and has drawn up major elements of spatial and cultural gene identification of traditional settlements, including geographic distribution, environmental pattern, cluster morphology, street space, and architectural features, and function orientation, creation concepts, value beliefs, and social conventions. On this basis, the article takes the traditional Qiang settlement in western Sichuan as an empirical case, systematically identifies and extracts 33 ‘morphological genes’ and 21 ‘cultural genes’ factors, and compares and analyzes the differences between them and Han settlements. It provides theoretical and methodological support for the identification, protection, sustainable development, and inheritance of the landscape features, elements, and genes of traditional settlements in China.