Gibberellins (GA) are involved in seed development and E3 ubiquitin-ligases actively participate in GA perception and signal transduction. TaGW2-6A encodes a RING E3 ubiquitin-ligase that negatively regulates grain size. Therefore, Chinese Spring (CS) and its TaGW2-6A allelic variants (NIL31) were investigated to elucidate the relative contribution of GA to the regulation of seed development in wheat. The expression levels of GA biosynthesis and response genes were higher in NIL31 than CS, especially those of GA 3-oxidase and GASA4. The expression of TaGW2-6A exhibited the opposite pattern compared with those of the GA biosynthesis and response genes in CS and NIL31. The results showed that the GA content of NIL31 was significantly higher than that of CS. Thus, TaGW2-6A had a negative relationship on GA synthesis and response genes. Moreover, after GA treatment, CS and NIL31 exhibited the opposite phenotypes and GA contents. These results demonstrate that allelic variation in TaGW2-6A increases the seed size via the GA hormone pathway. Transcriptional analysis and cytological analysis showed that TaGW2-6A allelic variants regulated GA synthesis via GA 3-oxidases, thereby leading to the higher expression of GASA4 to control endosperm cell elongation and division during grain filling. Finally, germination experiments were performed to elucidate the relationships between TaGW2-6A and GA synthesis and response genes in wheat with full fertility. These results provide new insights into the effects of the ubiquitination system mediated by TaGW2-6A on the GA hormone signaling pathway, thereby improving our understanding of the role of TaGW2-6A in seed development in wheat.