A method for altering the ratio of proteins/lipids in crop seeds utilizing the antisense gene, comprising the steps of: (1) cloning the gene for the phosphoenopyruvate carboxylase or acetyl-CoA carboxylase, or the fragment thereof; (2) constructing the corresponding antigene; (3) introducing the said antigene into the cells of the rapeseeds, so that the activity of the phosphoenopyruvate carboxylase or the acetyl-CoA carboxylase being important for the protein synthesis is changed, the flow direction of the common substrate, PEP, can be controlled, so that the proteins/lipids in the seeds is altered. The application can be used to alter the proteins/lipids in the crop seeds.