Wild and cultivated soybeans from different areas of China were used as materials for paraffin cross-sections of the juncture between the root elongation and maturation zones of wild and cultivated soybeans during the seedling stage. It was found that the casparian band of the endodermis and duct of metaxylem in the anatomical structure of the cultivated soybean developed faster than those of the wild soybean. Rapid development of these structures sped up transmission and enhanced support capacity. Meanwhile, two-dimensional electrophoresis was adopted to analyze the differences between the wild and cultivated soybean populations in terms of protein expression during the seedling stage. Our results showed that expression levels of 28 proteins from among the wild and cultivated soybean populations were significantly different from one another. In the cultivated population, the protein expression levels were up-regulated in four protein spots and down-regulated in 24 protein spots. Down-regulated proteins were associated with secondary metabolites and metabolism of antibiotics. Decrease in the expression these proteins may speed up nodule formation. These results showed that early growth and development of the cultivated soybean roots occurred at a significantly faster rate than those of the wild soybean. The increased rates of these processes accelerate root shape formation and improve root function. In conclusion, this study systematically explored the anatomical structure and differentially expressed proteins of roots between wild and cultivated soybean, and differentially expressed proteins identified here will be the valuable resource for studying soybean root differences resulting from domestication.