Here, we compare the molecular mechanism of soybean heterosis through the differential expression of basic cloning. Specifically, we cloned 22 differentially expressed cDNA fragments from hybrid combinations of Jilin 38 x EXP (which had obvious yield advantages) and their parents. In addition, we compared the homology of these fragments and predicted their functions. Cloning differentially expressed genes included the identification of the calmodulin binding protein, 18S ribosomal gene, 26S ribosomal gene, soybean satellite DNA, soybean acid phosphatase, soybean chlorophyll a/b-binding protein II (Cab-6) gene, soybean chloroplast PI 437654 gene, soybean PPR protein gene, and other fragments with unknown functions. In conclusion, the cloning and functional prediction of differentially expressed soybean genes in this study is anticipated to provide valuable information for studies on the molecular mechanism of heterosis.