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Determining the mechanisms that drive phenotypic and genetic divergence by species has been a central topic in evolutionary biology for many years. However, the relative contributions of isolation by distance (IBD) and environment factors to species divergence are largely unknown in perennial herbs in East Asia. In this study, we collected population genetic samples of the cold‐tolerant perennial herb Notopterygium oviforme R. H. Shan in central China. We integrated the population transcriptomes, whole chloroplast genomes, genotyping‐by‐sequencing, microsatellite markers, and ecological factors to determine the relative contributions of geography, climate, and soil factors to genetic, chemical, and phenotypic divergence. A clear genetic distinction was identified between the West Qinling and East Qinling Mountains geographical groups of N. oviforme based on various molecular datasets. Interestingly, obvious niche conservation might have been responsible for the similarity of most of the leaf functional traits in the two groups. Multiple matrix regression with randomization analysis showed that the spatial intraspecific divergence pattern was mainly due to IBD rather than isolation by environment. In addition, transcriptomic expression divergence and some ecological factors have played key roles in intraspecific lineage differentiation. Approximate Bayesian Computation showed that both lineages have experienced historical population expansion and recent range contraction. Molecular dating suggested that intraspecific divergence was closely associated with dramatic uplifts of the Qinling Mountains in East Asia. These results demonstrate that geographical, geological, and environmental factors together shaped cryptic intraspecific diversification and shifts in the population dynamics of the perennial cold‐tolerant herb N. oviforme. [ABSTRACT FROM AUTHOR]