Polyploids recurrently emerge in angiosperms, but most polyploids are likely to go extinct before establishment due to minority cytotype exclusion, which may be specifically a constraint for dioecious plants to evolve polyploid populations. Investigations into the frequency and distribution of polyploids in natural populations is thus necessary for understanding polyploid evolution in plants. This study determined the ploidy levels of 28 populations and 351 individuals of Salix polyclona, and identified the type of polyploidy (auto- vs. allo-) using whole genome re-sequencing data. We further investigated the phylogeny, population genetic diversity and species range shifts to explore the origin and spatiotemporal evolution of the polyploid complex. Our analyses revealed a high frequency (52%) of autopolyploids in it with a clear geographic distribution confined to the western part of its range where complex mountain systems create higher levels of environmental heterogeneity. Comparisons of diploid male and female genomes suggested a female heterogametic sex-determining factor on chromosome 15, which likely also acts in the dioecious polyploids. Fossil-calibrated phylogeny showed a more recent diversification of the polyploids (ca. 2.3 Ma) than the diploid (ca. 6.2 Ma), and population demographic histories largely corroborated the geological and climatic history of the region. Our results suggest that climatic oscillations and uplift of eastern Qinghai-Tibetan Plateau and the connecting mountains may have facilitated the preservation and establishment of polyploid populations. This study provides an example of the evolution of a diploid-polyploid complex in a willow species and illustrates a role of polyploidization in mountain biodiversity.