The FAB mass spectrometry (MS)/enantiomer labeled (EL) guest method is one of the useful technique to easily evaluate chiral discrimination ability of a chiral host (H) toward chiral guests (GR ῌ , GS῍d n ῌ ). In this paper, the matrix dependency of the relative peak intensity (IRIS) of the diastereomeric host῍guest complex ions [(Hῌ GR)ῌ and (HῌGS῍d n ) ῌ ] was investigated (host, MeFruNys; guest, Phe-O-iPr ῌ ). The IRIS values of spectra measured using NBA, NPOE, and DTDE matrices agreed almost with the ratio of concentrations of the complex ions calculated from the association constants (KR and KS) in chloroform at 298 K. While, the IRIS values of spectra using glycerol matrix reached almost unity. It was assumed that the IRIS values depend upon the matrices used since the di#erence of solvation ability of the matrices a#ects the actual concentration of the guest concerning in the complexation. And then, it was recommended that NBA is the best matrix for chiral recognition mass spectrometry studies.