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<i>AP3</i> has been studied and is reported to affect structural changes in floral organs in various plants. However, the function of the soybean <i>AP3</i> genes in flower development is unknown. Here, the full-length cDNA sequence of <i>GmAP3</i> was obtained by RACE and it was verified that it belongs to the MADS-box subfamily by a bioinformatics analysis. The expression of <i>GmAP3</i> is closely related to the expression of essential enzyme genes related to flower development. Yeast two-hybrid assays demonstrated that GmAP3 interacts with AP1 to determine the identity of flower organ development. A follow-up analysis showed that overexpression of the <i>GmAP3</i> gene advanced flowering time and resulted in changes in floral organ morphology. The average flowering time of overexpressed soybean and tobacco plants was 6–8 days earlier than that of wild-type plants, and the average flowering time of gene-edited soybean and tobacco plants was 6–11 days later than that of wild-type plants. In conclusion, <i>GmAP3</i> may directly or indirectly affect the flower development of soybean. The results of this study lay the foundation for further research on the biological functions of MADS transcriptional factors in soybeans.