Ancient whole-genome duplication (WGD) or polyploidization is prevalent in plants and has played a crucial role in plant adaptation. However, the underlying genomic basis of ecological adaptation and subsequent diversification after WGD are still poorly understood in most plants. Here, we report a chromosome-scale reference genome assembly for the genus Orinus (Orinus kokonorica as representative) and preformed comparative genomics with its closely related genus Cleistogenes (Cleistogenes songorica as representative), both belonging to a newly named subtribe Orininae of the grass subfamily Chloridoideae. The two genera may share one paleo-allotetraploidy event before 10 million years ago, and their two subgenomes display neither fractionation bias nor global homoeolog expression dominance. Recent expansion of transposable elements and enormous contraction in gene families in O. kokonorica have maintained a similar genome size compared to C. songorica. Further comparative genomic analyses reveal substantial genome rearrangements and extensive structural variations (SVs) between the two species. With comparative transcriptomics, we demonstrate that functional innovations of orthologous genes have played an important role in promoting adaptive evolution and diversification of the two genera after polyploidization. In addition, copy number variations in flower and rhizome development related genes and extensive SVs between orthologs may contribute to the morphological differences between the two genera. Our results provide significant new insights into the adaptive evolution and subsequent diversification of the two genera after polyploidization.