The present invention relates to a novel thermostable N-acylamino acid racemase (NAAAR) isolated from Deinococcus radiodurans NCHU1003, the coding sequence and the preparation thereof. The present invention also discloses the process for preparing highly optically pure L-amino acids, such as L-homophenylalanine (L-HPA) and the derivatives thereof, from N-protected amino acid by using the novel NAAAR combined with L-N-carbamoylase.