In this study,the chemical fingerprints of roots,leaves,fruits and stems of Macleaya cordata were established by HPLC,and the contents of protopine,allocryptine,sanguinarine and chelerythrine were determined;orthogonal partial least squares discriminant analysis (OPLS-DA) was used to evaluate the quality of roots,leaves and fruits of M. cordata.The fingerprint results showed that 17 batches of root samples were calibrated with 10 common peaks,14 batches of leaf samples were calibrated with 9 common peaks,14 batches of fruit samples were calibrated with 9 common peaks,and 10 batches of stem samples were calibrated with 6 common peaks.The order of the total contents of four alkaloids in different organs of M. cordata is:fruit > root > leaf > stem;the contents of the above four alkaloids were higher in the fruit and were lower in the stem;the contents of protopine and allocryptine higher in the root and leaf.The resources of M. cordata roots are large,and the contents of protopine and allocryptopine are higher than those of fruits and leaves,it can be developed and utilized with M. cordata fruits and leaves as the above alkaloid extraction raw materials.The results of OPLS-DA showed that if VIP > 1,allocriptine and chelerythrine could be used as potential quality markers of M. cordata roots;sanguinarine and chelerythrine can be used as potential quality markers of M. cordata leaves;protopine,allocryptine and sanguinarine can be used as potential quality markers of M. cordata fruits.The results of this study provide a research basis for the identification and evaluation of the roots,leaves,fruits and stems of  M. cordata and the development and utilization of M. cordata roots.