A molecular simulation study is reported to investigate liquid chromatographic separation in metal-organic framework MIL-101. Two mixtures are considered: three amino acids (Arg, Phe, and Tip) in aqueous solution and three xylene isomers (p-, m-, and o-xylene) dissolved in hexane. For the first mixture, the elution order is found to be Arg > Phe > Tip. The hydrophilic Arg has the strongest interaction with the polar mobile phase (water) and the weakest interaction with the stationary phase (MIL-101), and thus transports at the fastest velocity. Furthermore, Arg forms the largest number of hydrogen bonds with water and possesses the largest hydrophilic solvent-accessible surface area. For the second mixture, the elution order is p-xylene > m-xylene > o-xylene, consistent with available experimental observation. With the largest polarity as compared to p- and m-xylenes, o-xylene interacts the most strongly with the stationary phase and exhibits the slowest transport velocity. For both mixtures, the underlying separation mechanism is elucidated from detailed energetic and structural analysis. It is revealed that the separation can be attributed to the cooperative solute solvent and solute framework interactions. This simulation study, for the first time, provides molecular insight into liquid chromatographic separation in a MOF and suggests that MIL-101 might be an interesting material for the separation of industrially important liquid mixtures.