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(+)-(18-Crown-6)-tetracarboxylic acid (18C6H4) is used as a chiral selector for various amino acids, where the l-isomer is usually eluted prior to the d-isomer in HPLC using 18C6H4-linked column. To clarify the structural scaffold of (+)-18C6H4 responsible for chiral separation of amino acids, we have previously investigated the interaction mode between (+)-18C6H4 and amino acids using X-ray analysis. However, no conclusive results could be obtained to explain the reverse elution order in the case of serine and to establish a general separation rule of chiral amino acid by (+)-18C6H4 in HPLC. Thus, to clarify the exceptional result obtained with serine and to set a general separation rule, interaction between (+)-18C6H4 and α-amino-n-butyric acid, valine, and alanine, as methyl substitutes of the methyl groups for the hydroxy groups of serine and threonine, and the simplest chiral amino acid, respectively, was investigated both in solution and solid states. Consequently, it was found that an asymmetric bowl-like conformation of (+)-18C6H4 is necessary for chiral separation. This conformation is constructed by chiral-specific interaction between the Cα–H groups of the amino acid and the polar oxygen atoms of (+)-18C6H4. It was also found that the exceptional reverse elution observed with serine is due to additional interaction between the polar groups of the amino acid side chain and (+)-18C6H4.