The present invention relates to a field of biotechnology. It discloses a novel amino acid sequence of recombinant human bone morphogenetic protein-2 (rhBMP-2) and encoded nucleotide sequences thereof, and a method for preparing rhBMP-2. In the present invention, by further optimizing the nucleotide sequence of rhBMP-2, novel amino acid sequence of rhBMP-2 that can express good ectopic induced osteogenic activity and has good renaturation and purification effect is screened out. The engineered bacteria constructed by the present invention can induce the production of recombinant rhBMP-2 protein with an expression level of about 55%, and the produced target protein is more easily denatured and purified than the existing recombinant rhBMP-2, with better denaturation and purification effect and higher osteoinductive activity.