Countercurrent chromatography (or counter-current chromatography, CCC) is a unique support-free liquid-liquid partition chromatography. Since it was invented by Y. Ito in 1960s, CCC has been widely accepted and applied as popular separation and purification technique for natural and synthetic complex. However, up to date there is little study to address on hydrophobic and hydrophilic interactions in CCC process, although hydrophobic interaction chromatography (HIC) and hydrophilic interaction chromatography (or hydrophilic interaction liquid chromatography, HILIC) as solid-support chromatographic techniques are widely applied at different stages of downstream processing. In fact, hydrophobic and hydrophilic interactions might be more popular in CCC separation than that in the liquid chromatography. For example, adding small solvents or additives in two-phase solvent systems may change significantly hydrophobic or hydrophilic interactions between solvents and solutes. Normally, CCC separation employs a light and hydrophobic organic phase as the stationary phase, and a heavy and hydrophilic aqueous phase as the mobile phase. Hydrophobic interactions between the solvent system and solutes (targets) will increase the partition coefficients (K values) of solutes and lengthen retention time, while hydrophilic interactions will reduce the K values and separation time. In this work, we aim to provide a general insight on the hydrophobic and hydrophilic interactions in CCC separation. We also highlight the current advances in utilizing the hydrophobic and hydrophilic interactions for K-targeted CCC separation and purification.