Tibetan hulless barley (qingke) grains are becoming more popular because of their high nutritional benefits. Comparative metabolomics and proteomics analyses of qingke grains (at 16, 20, 36, and 42 days after flowering) were conducted to explore the metabolic dynamics during grain filling and compare the differences in quality among three different varieties, Dulihuang, Kunlun 14, and Heilaoya. A total of 728 metabolites and 4864 proteins were identified. We first found that both the metabolite and protein profiles were more closely associated with the grain developmental stage in each cultivar than across different stages in a single cultivar. Next, we focused on the energy metabolism and biosynthesis pathways of key quality components, such as flavonoids, starch, and β-glucans in qingke grains. Quantitative analysis revealed significant variation in the abundance of cellulose synthase-like enzyme (CslF) among the three cultivars. Notably, Heilaoya displayed substantially lower CslF6 levels at 36 and 42 DAF than Kunlun 14 and Dulihuang did. These observed differences in CslF6 abundance may represent a key regulatory mechanism underlying the distinct β-glucan biosynthesis patterns among the three cultivars. Collectively, our results enhance the understanding of metabolic networks involved in qingke grain development and serve as a foundation for advancing breeding studies.