Nitrogen fertilizer is a critical determinant of grain yield and seed quality in wheat. However, the mechanism of nitrogen level during seed production affecting wheat seed vigor and seedling establishment at the transcriptome level remains unknown. Here, we report that wheat seeds produced under different nitrogen levels (N0, N168, N240, and N300) showed significant differences in seed vigor and seedling establishment. In grain yield and seed vigor, N0 and N240 treatments showed the minimum and maximum, respectively. Subsequently, we used RNA-seq to analyze the transcriptomes of seeds and seedlings under N0 and N240 at the early stage of seedling establishment. Gene Ontology (GO) term enrichment analysis revealed that dioxygenase-activity-related genes were dramatically upregulated in faster growing seedlings. Among these genes, the top three involved linoleate 9S-lipoxygenase (Traes_2DL_D4BCDAA76, Traes_2DL_CE85DC5C0, and Traes_2DL_B5B62EE11). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that pathways involved in nutrient mobilization and the antioxidant system showed enhanced expression under N240. Moreover, seeds with faster growing seedlings had a higher gene expression level of α-amylase, which was consistent with α-amylase activity. Taken together, we propose a model for seedling establishment and seed vigor in response to nitrogen level during seed production.