Sheepgrass (Leymus chinensis ((Trin.) Tzvel)) is an important perennialforage grass that is widely distributed in the Eurasia steppe. The seed germination percentage show significant variation among the different germplasm in sheepgrass. However, the underlying molecular mechanisms of distinct germination during seed development are still mostly unknown. Here, we performed comparative transcriptomic analyses of high seed germination percentage (H) and low seed germination percentage (L) at 14, 28, and 42 days after pollination. After comparing 3 consecutive development stages, 9255, 5366, and 4306 genes were found to be significantly differently expressed between H and L. Pathway analysis indicated that transcripts related to starch and sucrosemetabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, amino sugar and nucleotide sugar metabolism, and photosynthesis were significantly changed between the two germplasm at three stages. ABA and GA metabolism- and signaling transduction-related genes were differentially expressed between two germplasm at development stages, suggesting that the reduced signaling of GA and ABA is likely to be related to seed germination and dormancy in sheepgrass. We also identified 81 transcription factor (TF) families, and some TFs genes such as NAC48, NAC78, WRKY80, ZnFP, C3H14 and ILR3 were significantly differential expressed in two germplasm. Our results provide insights into seed development, germination and dormancy in sheepgrass at the transcriptional level.