Chun & S.K. Lee is a rare and endangered tree species endemic to the karst forests of southwestern China. Its seeds are rich in nervonic acid, a compound of significant ecological and economic value. However, habitat fragmentation, overharvesting, and climate change have imposed severe survival pressures on this species, leading to a risk of genetic diversity loss. In this study, we employed genotyping-by-sequencing (GBS) to investigate the genome-wide genetic diversity and population structure of 89 individuals from 16 natural populations. A total of 332,551 high-quality single nucleotide polymorphisms (SNPs) were obtained. The results showed moderate genetic diversity, with populations in Guangxi exhibiting significantly higher nucleotide diversity than those in Yunnan. Population structure analyses identified six genetic clusters that corresponded closely to their geographic distribution, indicating that geographic isolation is the main driver of genetic differentiation. Mantel tests revealed a highly significant positive correlation between genetic and geographic distances but no correlation with environmental distance, representing a typical isolation-by-distance (IBD) pattern. Redundancy analysis (RDA) identified 4,361 SNPs significantly associated with environmental variables suggesting potential local adaptation signals. Demographic reconstruction revealed that began a sharp and continuous decline in effective population size approximately 30 kya, likely triggered by climatic fluctuations during the Last Glacial Maximum. These findings provide valuable insights for the conservation, restoration, and regional management of this ecologically and economically important species.