In the present paper, different mensurations of Fourier transform infrared spectra for the analysis of Paeonia lactiflora Pall. were compared. FTIR mensurement was applied to the analysis of quality of xylem and outer layer of Paeonia lactiflora Pall. from native habitat. The results revealed that the chemical contents are the same in both the xylem and outer layer of Paeonia lactiflora Pall.. But outer layer has less paeoniflorin and its derivatives than in xylem of Paeonia lactiflora Pall. Different habitats of xylem of Paeonia lactiflora Pall.. were Hanzhou, Anhui and Sichuan. The results indicated that the quality with habitat in Zhejiang is the best among the three.