Five samples of Cistanches Herba from different places were analyzed by HPLC-ESI-MS and FTIR methods.The effective compositions in Cistanches Herba including cistanoside A,echinacoside,acteoside ,isoacteoside,2’-actylacteoside,cistanoside C and tubluoside B were determined by HPLC-MS.The common peak ratio and variant peak ratio were calculated by FTIR spectroscopy of the five samples and the dual index sequence of common peak ratio and variant peak ratio were established.The results showed that the evaluation results of the samples by the two methods were the same.The general fake plant Cynomorii Herba could be identified by FTIR.HPLC-ESI-MS,which has high sensitivity and rapid determination procedure,can be used to evaluate quality of Cistanches Herba by quantitative analysis of the primary compositions.FTIR is a non-destructive analysis method without complicated extraction and separation procedures to the samples.The absorption strength and the absorption shape were the synergistic effect of the functional groups and the nestification of the components in Cistanches Herba.The provided method has some advantages such as rapid analysis process,good reproducibility,non-destructive,small quantity of sample,simple treatment,good specificity,low-cost and environment-friendly.The method meets the trend of complex analysis and whole analysis for the Chinese medicines.Combination of FTIR and HPLC-ESI-MS was a good method for identification and evaluation of quality of Chinese medicines.