Starch is the final product of photosynthesis and the main storage form in plants. Studies have shown that there is a close synergistic regulatory relationship between ABA signal transduction and starch biosynthesis. In this study, we employed RNA sequencing (RNA-Seq) to investigate transcriptomic changes of the Euryale ferox seeds treated by exogenous ABA. The differentially expressed genes engaged in the “Starch and sucrose” and “TCA cycle” pathway. Furthermore, the key transcription factor EfABI4 in ABA signaling pathway and the key genes of starch biosynthesis (EfDBE1, EfSBE2, EfSS1, EfSS2, EfSS3, EfSS4 and EfGBSS1) were significantly up-regulated. Further, the Euryale ferox plant was treated with ABA, it was found that the total starch content of Euryale ferox seeds at different development stages was significantly higher than that of the control, and the key genes of starch synthesis in Euryale ferox seeds were also significantly up-regulated. Finally, yeast one-hybrid and dual luciferase assay proved that EfABI4 can promote the expression of EfSS1 by directly binding to its promoter. Subcellular localization results showed that EfABI4 protein was located at the nucleus and EfSS1 protein was located in the cytomembrane. These findings revealed that ABA promotes starch synthesis and accumulation by mediating EfABI4 to directly promote EfSS1 gene expression, which is helpful for understanding starch synthesis in seeds.