Obtaining purified nitrotoluenes from their mixture is significant but challenging due to their similar molecular sizes and physical properties. To overcome this challenge, here we report a stable, inexpensive and green-synthesized aluminium-based metal–organic framework (MIL-160) to separate the nitrotoluene mixtures. The appropriate pore size and pore environment permitted MIL-160 to exhibit a rare meta-nitrotoluene (m-NT) preference and always maintain the meta- > ortho- > para-nitrotoluene (m- > o- > p-NT) adsorption order in dynamic breakthrough and pulse modes as well as batch-mode adsorption. Theoretical calculations revealed that the abundant H/O atoms in the confined nanospace provided strong binding sites for selectively capturing nitrotoluene isomers. Specifically, due to difference in shape matching, the strongest host–guest interactions occurred in m-NT@MIL-160, followed by o-NT@MIL-160, and last p-NT@MIL-160. Notably, breakthrough experiments confirmed that a variety of binary and ternary mixtures can be separated via continuous adsorption. The dynamic adsorption stage of ternary mixture directly produced 0.33 mmol g−1 of pure p-NT, and the eluent in the desorption stage contained a high content of m-NT. Additional dynamic adsorption model fitting results indicated that the outstanding dynamic separation performance was also achieved from kinetic factors. These results lay the foundation for the effective separation of nitrotoluene mixtures.