At present, the separation of racemates is still a great challenge, since they are enantiomers, having similar chemical structures and physical properties. Here, we proposed a new strategy for efficiently separating chiral compounds, i.e., stereoselectively hydrolyzing the individual enantiomer of racemates via enzyme, followed by a simple magnetic separation using Fe3O4 nanoparticles, may implement a complete resolution of racemates. In this work, d-aminoacylase was selected as enzyme, and phenylalanine and methionine as chiral models. The use of d-aminoacylase can hydrolyze d-enantiomer, while l-enantiomer cannot. Magnetic nanoparticles of Fe3O4@SiO2-NH2-COOH composites were designed and synthesized for the amidation reaction with the hydrolyzed d-amino acids from the mixture. With the help of a magnetic field, d-form amino acids can be readily separated at a large scale and the resultant resolving performances indicated that this method exhibited a higher selectivity, compared with common chiral separation techniques. The enantiomeric excess (e.e.) values are 75% and 98% for racemic N-acyl-phenylalanine and methionine, respectively, which solely rely on the hydrolysis capability of used enzymes. This result suggests that our method is feasible, simple, easy to scale-up and high-efficient for the chiral resolution. These findings demonstrate that this strategy could provide new opportunities for improving enantioseparation performances for a host of enantio- and bio-substance with both high-yield and high-selectivity.