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The <i>UNUSUAL FLORAL ORGANS</i> (<i>UFO</i>) gene is an essential regulatory factor of class B genes and plays a vital role in the process of inflorescence primordial and flower primordial development. The role of <i>UFO</i> genes in soybean was investigated to better understand the development of floral organs through gene cloning, expression analysis, and gene knockout. There are two copies of <i>UFO</i> genes in soybean and in situ hybridization, which have demonstrated similar expression patterns of the <i>GmUFO1</i> and <i>GmUFO2</i> genes in the flower primordium. The phenotypic observation of <i>GmUFO1</i> knockout mutant lines (<i>Gmufo1</i>) showed an obvious alteration in the floral organ number and shape and mosaic organ formation. By contrast, <i>GmUFO2</i> knockout mutant lines (<i>Gmufo2</i>) showed no obvious difference in the floral organs. However, the <i>GmUFO1</i> and <i>GmUFO2</i> double knockout lines (<i>Gmufo1ufo2</i>) showed more mosaic organs than the <i>Gmufo1</i> lines, in addition to the alteration in the organ number and shape. Gene expression analysis also showed differences in the expression of major ABC function genes in the knockout lines. Based on the phenotypic and expression analysis, our results suggest the major role of <i>GmUFO1</i> in the regulation of flower organ formation in soybeans and that <i>GmUFO2</i> does not have any direct effect but might have an interaction role with <i>GmUFO1</i> in the regulation of flower development. In conclusion, the present study identified <i>UFO</i> genes in soybean and improved our understanding of floral development, which could be useful for flower designs in hybrid soybean breeding.