Using pepper fruit of Hainan as raw material and 95% ethanol as solvent, the alkaloid in pepper is extracted with reflux method in this paper. The piperonylic acid is removed by adjusting the pH; the fat-soluble substance being removed by adding ethyl ether; the piperine alkaloid being purified with acetone by recrystallization anddetected with HPLC, as well as characterized with IR. The characterizations of piperine are discussed. Meanwhile, B3LYP/6-31G (d,p) method of DFT is applied to optimize the structure, calculate frequency and energy of pepper alkaloid, then obtain four kinds of configurations (configuration Ⅰ as Piperine, configuration Ⅱ as Iso Piperine, configuration Ⅲ as Iso Chavicine, configuration Ⅳ as Chavicine) with 64 kinds of stability conformational structure. The distribution of the thermodynamic equilibrium of stable conformations of four kinds of configurations of the molecular is calculated with Gibbs free energy at room temperature (298.15 K). And IR spectra of the experimental were compared with the IR spectra of the theoretical. The results show that the alkaloid extracted from pepper is mainly conformer 1 in configuration Ⅰ, that is, Piperine; after purifying, the content of piperine is 7% with the purity of 99%. With analysis, the methods of extraction, separation and purification of piperine in this paper achieve good results. Established models are in good agreement with the experimental results. This research is of great significance in guiding extracting process, building structural model and the characterization and application of piperine.