Phylogenetics, originally developed from the life sciences, investigates the entire lifecycle of organisms, thereby uncovering the evolutionary traits and patterns of their subjects of study. Spatial-Temporal characteristics of traditional settlement landscape from the perspective of phylogenetics are helpful to analyze the spatial characteristics of traditional settlement landscape from the dual dimensions of the constantly updated dynamic construction process and the synchronic characteristics formed by spatial superposition, and further clarify the mechanism affecting the Spatial-Temporal characteristics of traditional settlement landscape. Taking the traditional commercial settlement Baimazhai village in Fengcheng, Jiangxi as the research object, the historical environment is regarded as a process of dynamic construction, restoring the historical landscape form of settlements under the influence of "dual commercial activities" from a phylogenetics standpoint, and carried out for the construction of historical landscape of the settlement space is "time evolution" and "spatial congruence" models from the perspective of commercial trade, and presenting a complex system of "multilayered spatiotemporal integration". The results show that: 1) From the Wanli period of the Ming Dynasty to modern times, Baimazhai village saw major geographical modifications as a result of natural circumstances, sociocultural causes, and economic growth, considering the impact of Baimazhai village's commercial activities, this study projects historical elements observed in the synchronic state into the diachronic evolution of the village, thus reconstructing its historical spatial development. The evolution process has gone through four stages: the relocation of the foundation period: the beginning of the dragon vein and the separation of sides; During the Wanli period of the Ming Dynasty: the houses are lined up horizontally and in a row; During the Guangxu period of the Qing Dynasty: distributed like a comb and clearly partitioned; Modern: differentiation and integration with blurred partitions. 2) In terms of site selection and construction, Baima Village's ancestors stressed the harmonious relationship of humans and environment, landscape care/Yin-Harmonizing/ancestral temple ceremonial/social interaction/defensive barrier, clan faction, and housing structure landscape space. These zones gradually overlapped and blended, resulting in a village environment distinguished by its proximity to natural landscapes, a rich historical setting, and a community living in harmony and prosperity. 3) The historical landscape of the settlement presents the following three characteristics, namely, "circle-based" + "orderly" landscape space system, "center + group" patriarchal cultural landscape space, and "village-fort-style" + "row-type" combination form. 4) Baimazhai village is more than just a traditional settlement; its evolution is governed by multiple interwoven mechanisms. Firstly, endogenous evolution is primarily fueled by clan kinship, serving as both the evolutionary drive and the connective tissue for spatial development, fundamentally shaping the expansion of social spaces within the settlement. Secondly, embedded evolution is driven by distinctive features, characterized by the strategic incorporation of functional and event-specific spaces, tailored to suit local conditions. The third mechanism, mediated evolution, is propelled by historical events, resulting in the integration of institutional and anticipatory spaces designed for collaborative engagement. Baima Village's development is influenced both by its internal clan dynamics and by external pressures such as merchant guild activities, warfare, and resource disputes. These elements are projected into the settlement's form through its spatial organization, where they interact and coalesce to shape the overall spatial configuration of the settlement, imbuing it with distinct regional cultural significance. Using phylogenetic approaches to investigate its geographical development process, features, and driving forces is conducive to fully understanding the value characteristics of dual-merchant settlements and further deepening the theoretical research system of traditional settlements landscape.