Abstract: Crop molecular design breeding has shown more advantages over other breeding methods,and is becoming the mainstream of crop breeding technology for the future.The rapid progress of soybean genomics and transgenic technology provides a solid foundation for soybean molecular design breeding.The challenge of soybean molecular design breeding in the future lies in developing the genotype-phenotype breeding models at system biology level.Soybean breeding work will remain for quite a long transition period from traditional breeding to marker-assisted breeding,transgenic breeding,and then to molecular design breeding while the molecular design breeding will play more and more important roles in soybean breeding.