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Shoot branching is one of the most variable determinants of crop yield, and the signaling pathways of plant branches have become a hot research topic. As an important transcription factor in the B3 family, NGATHA1 (NGA1), plays an important role in regulating plant lateral organ development and hormone synthesis and transport, but few studies of the role of this gene in the regulation of plant growth and stress tolerance have been reported. In this study, the <i>NGA1</i> gene was isolated from <i>Medicago truncatula (Mt)</i> and its function was characterized. The cis-acting elements upstream of the 5′ end of <i>MtNGA1</i> and the expression pattern of <i>MtNGA1</i> were analyzed, and the results indicated that the gene may act as a regulator of stress resistance. A plant expression vector was constructed and transgenic Arabidopsis plants were obtained. Transgenic Arabidopsis showed delayed flowering time and reduced branching phenotypes. Genes involved in the regulation of branching and flowering were differentially expressed in transgenic plants compared with wild-type plants. Furthermore, transgenic plants demonstrated strong tolerances to salt- and mannitol-induced stresses, which may be due to the upregulated expression of <i>NCED3</i> (<i>NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3</i>) by the <i>MtNGA1</i> gene. These results provide useful information for the exploration and genetic modification use of <i>MtNGA1</i> in the future.