Isolation of bioactive compounds from extracts of pharmaceutical plant is very important. In this work, copper benzene-1,3,5-tricarboxylate metal organic framework (Cu-BTC MOF) has been synthesized. It is used in separating of chamazulene from chamomile extract. The Cu-BTC MOF not only shows good chamazulene adsorption but also maintains good desorption properties. However, the research on this field is still new and the maturation of novel MOFs or the enhancements of known ones are required.The chamomile extract obtained after each stage of the treatments was carefully characterized by thin-layer chromatography (TLC), Fourier-transform infrared spectroscopy (FTIR), UV–vis spectrometry and gas chromatography-mass spectrometry (GC–MS). The morphology and the crystallinity of Cu-BTC MOF were investigated using scanning electron microscopy (SEM) and powder X-ray diffraction (PXRD), respectively. Breakthrough experiments in a column was investigated and the data was fitted with Bohart-Adams model. Monte Carlo simulation was conducted to investigate the preferential adsorption sites of Cu-BTC for chamazulene molecules.