Novel chiral layered molecular space L-(+)-leucine amidepropylamidephenylsilica (L-(+)-Leu-APAPhS) and D-(−)-alanine amidepropylamidephenylsilica (D-(−)-Ala-APAPhS) were synthesized through grafting L-leucine tert-butyl ester (L-Leu-OtBu) and D-alanine tert-butyl ester (D-Ala-OtBu), in layered carboxylpropylamidephenylsilica (CPAPhS), which was developed in our previous research, with regular carboxyl groups, and the tert-butyl ester as protective groups of carboxyls in amino acids was cleaved with dilute trifluoroacetic acid (TFA). The improved XRD response indicated that the two dimensional layered structure had been retained in L-Leu-APAPhS and D-Ala-APAPhS. The chiral behaviors of layered molecular spaces CPAPhS, L-(+)-Leu-APAPhS and D-(−)-Ala-APAPhS were investigated. DL-Alanine tert-butyl ester (DL-Ala-OtBu) was grafted in the achiral layered molecular space CPAPhS as enantiomer pair, even if 70% L-Ala-OtBu and 30% D-Ala-OtBu existed in the reaction solution. L-(+)-Leu-APAPhS and D-(−)-Ala-APAPhS represented better chiral selectivity for amino acids both in chiral selective reactions and chiral column chromatography experiments, and exhibited the potential of chiral layered molecular space with an amino acid structure for chiral molecular recognition and selection processes. The formation of L-Leu-APAPhS-L-Ala-OMe also exhibited potential for that multi-amino acid (peptide) can be grafted in CPAPhS to form layered molecular spaces with peptides.