The concept of cultural landscape genes of traditional settlements (CLGTS) was proposed by Chinese scholars in 2003. Since then, CLGTS has been playing a key role in capturing the deep-level geographic features of traditional settlements. However, there is a lack of work on covering CLGTS from the perspective of semiotics. Now, people are often involved in difficulties when they are trying to explore the nature of cultural landscapes of traditional settlements through using CLGTS. Obviously, it is of great significance to explore the concepts and methods of semiotic mechanism of CLGTS under the support of semiology. To lock this issue, we outline the dialectical features of CLGTS through the following five aspects. (1) For a given traditional settlement, its whole image at the macro-scale is in accordance with its cultural landscape genes at the micro-scale. (2) For the cultural landscape gene of a given traditional settlement, its core characterizations are in accordance with its appearance features. (3) For a given traditional settlement, its self-updating mechanism at local scale is in accordance with its global characterizations. (4) CLGTS can be treated as the scientific analysis method merged with the quantitative and qualitative approaches for dissecting the cultural features of traditional settlements. (5) For a given traditional settlement, its outstanding features of cultural landscape are in accordance with its rich cultural connotation. Then, this work proves the diversity of forms and complexity of spatial structures of CLGTS through ample examples. To some extent, this reveals the nonlinearity, self-organization, as well as self-iteration features of CLGTS. Based on the above, this research presents a conceptual framework of semiotic mechanism of CLGTS. Within the framework, we further summarize the symbols' main features, classifications, and expression ways of CLGTS. Through this work, we make clear the requisite theoretical conditions of making symbols of CLGTS by employing GIS. Ultimately, based on the aforementioned conceptual framework, this paper develops a prototype program for making symbols of CLGTS. The test results of the prototype program with a case of ancient village of Hunan Province show that it can run well in serving to establish a symbol database of CLGTS for a given region. Hence, this research proves that semiotic mechanism of CLGTS will make sense of perfecting the theory of CLGTS and forwarding its digital protection.