The aim of this work was to develop a new process for extraction and separation of polar and nonpolar compounds from natural materials using supercritical CO2 (SCCO2) in water. In this work, chlorogenic acid and caffeine from coffee beans were used as model compounds of polar and nonpolar compounds, respectively. Extraction and separation were conducted in three types of semicontinuous extractors with different sizes and flow types of CO2 and water. The effect of temperature and pressure in the separation mode using SCCO2 in flow and water in batch mode has been reported. Recovery of caffeine in the SCCO2 phase increased with decreasing temperature and increasing pressure. However, only the increasing pressure could promote the increasing recovery of caffeine and chlorogenic acid in water phases. The change of height of the nonpolar recovery section on the recovery of caffeine and chlorogenic acid in SCCO2 and water phases and on the separation factor has been studied using SCCO2 and water in co-current and counter-current flow modes. Recovery of caffeine and separation factor of caffeine from dilorogenic acid significantly increased with increasing height of nonpolar recovery section. The effect of temperature in counter-current type of separation on the recovery of caffeine and chlorogenic acid in SCCO2 and water phases exhibited different trend with batch type of separation. The counter-current type of separation was more effective compared to both batch and co-current types of separation. On the basis of the results of this work, it is suggested to design longer extractor columns with a higher nonpolar recovery section in the counter-current type in order to increase separation efficiency.