Abstract: In addition to the famous historical and cultural towns and traditional villages, there are still plentiful contiguous villages and towns with spatial characteristics in China's rural areas, which are also important carriers of regional historical contexts and spatial transitions. Current planning and regulation systems are lack of effective guidances and regulation methods for the protection and transformation of such spaces. So, it is vital to develop key technologies for the protection and utilization of spatial genes in characteristic villages and towns. Taking the typical area of characteristic villages and towns in southeastern China, the middle and lower reaches of the Minjiang River Basin, as an example, this study adopts the composite method of spatial gene identification, evaluation, protection, and utilization to carry out multi-spatial scales, multi-elements categories and long-duration history analysis of characteristic villages and towns. The research proposes to identify and extract the key spatial genes of regional constructions and settlement formations, and to translate and regenerate traditional spatial genes from the two dimensions of spatial gene feature identification and zeitgeisty adaptive evaluation. On this basis, it puts forward an optimized solution and reference for rural locality protection and regeneration of characteristic villages and towns around China.