Soybean molecular breeding represents development of overall soybean breeding. It entails marker-assisted selection breeding, transgenic breeding and crop breeding by design. By comprehensive use of methods and theories on genomics, bioinfomatics, computational and genetic breeding etc, the soybean can be manipulated at multiple levels from phenotypes to molecular so that breeding efficiency can be increased tremendously and directional improvement can be finally realized. In this paper, we mentioned the pioneer scientists, who contributed to the marker-assisted selection breeding, transgenic breeding and crop molecular design in China, tired to review the key research progress in China and compared with the advanced levels in the world. But we apologized to those not mentioned scientists who made great progress in related fields due to our limited knowledge. It was obvious that the accumulation of research data in China was less than that in other countries, but some differences were not as vast. One such was the characterization of cloned soybean genes.Scientiests transformed them back into the soybean itself, a great progress in China, one that could compete with the advanced world levels. The author indicated that developing trends for soybean molecular breeding will be multi-informational and will intergrate a genetic map, large scale discovery of genes, high efficiency of molecrlar breeding technique and systematics of molecular breeding theory.