Piper longum L. is an edible Traditional Chinese Medicine (TCM), and used as mongolian, tibetan and uyghur medicines, and listed in the Chinese Pharmacopoeia to treat disease, such as stomachache and diarrhoea, which is also used as spice and flavoring. Active Ingredients in Piper longum L. are amide alkaloids. While reported articles mostly focus on the contents of piperine or piperlonguminine by high performance liquid chromatography, and the quality control method is relatively simple and lack of holism and innovation. This paper analyzed six batches of Piper longum L. from four areas by FTIR and HPLC fingerprint. The common peak ratio and variant peak ratio were calculated by FTIR spectroscopy of the six samples, and the dual index sequence of common peak ratio and variant peak ratio were established. Entire compositions of Piper longum L. were analyzed by HPLC fingerprint, and the contents of piperine or piperlonguminine were listed. The result showed that the evaluation results of the samples by the two methods were mutual corroboration. Six batches of Piper longum L. contained similar compositions with relatively stable quality. Among them, Piper longum L. rised in Yunnan (S1) was different from the other five batches. Results showed that common peak ratio and variant peak ratio of IR could evaluate the quality of the compositions in TCM integrally and comprehensively, as well as HPLC fingerprint. while the HPLC fingerprints only showed the compounds with ultraviolet absorption at 254 nm. Therefore, IR was suitable to analyze the composition system of complex TCM. The absorption peak strength and peak shape in the IR are the results of the interaction of various functional groups and generated by the superposition of various chemical components in the infrared spectrum of Piper longum L., The HPLC fingerprint of Piper longum L. showed 17 common peaks and the similarity verified the results of IR. Contents of piperine and piperlonguminine were higher in Piper longum L. from Bozhou and Guangxi than Yunnan and Hainan, and results demonstrated single component was difficult to represent the entire quality of TCM. This paper reported the FTIR and HPLC fingerprint methods in the quality control of Piper longum L. for the first time, and the two methods were simple and rapid with small usages, and complemented each other. The methods provided research basis for chemical compositions, quality controls, developments and application of Piper longum L., and probed the influence of planting resources on herbal medicines.