Awns are crucial spike traits in Poaceae plants and are closely associated with seed development. Elymus nutans Griseb. is a high-quality alpine forage and an essential grass species for ecological restoration. To reveal the regulatory mechanism of awns on thousand seed weight in E. nutans, 20 E. nutans germplasm accessions were used as experimental materials in this study. Superior germplasms were screened via phenotypic correlation analysis. The screened superior germplasm was subjected to awned and de-awned treatments. Physiological indicators during seed development under the two treatments were measured at the milk stage, dough stage, and full ripe stage, and transcriptome sequencing was further used to identify the core regulatory pathways and key genes. The results showed that awn length was extremely significantly positively correlated with thousand seed weight (p < 0.01), and the optimal germplasm PI 655186 with superior awn length and thousand seed weight was obtained. Compared with the de-awned treatment, the awn-retained treatment significantly increased the contents of soluble sugar and starch in seeds from the milk stage to the dough stage and enhanced the activities of SOD, CAT, and POD to maintain redox homeostasis. Transcriptome analysis indicated that differentially expressed genes were significantly enriched in pathways including starch and sucrose metabolism and ascorbate and aldarate metabolism, among which UGDH, GLCAK, VTC2_5, and APX were identified as key genes regulating seed development, and WGCNA showed that the brown module was significantly correlated with soluble sugars and starch, with hub genes consisting of seven 60S ribosomal proteins and one prolyl 4-hydroxylase. In conclusion, awns positively affect the thousand seed weight of E. nutans seeds by promoting the synthesis of storage substances, optimizing the antioxidant enzyme system, and regulating the ascorbate and aldarate metabolism pathway and the expression of hub genes. These findings clarify the physiological and molecular mechanisms by which awns regulate seed thousand seed weight and provide a theoretical basis and gene resources for the innovation of high-yield and high-quality germplasms of alpine forage grasses.