Peak broadening and peak tailing are common but rebarbative phenomena that always occur when using metal-organic frameworks (MOFs) as stationary phases. These phenomena result in diverse "low-performance" MOF stationary phases. Here, by adjusting the particle size of MOF stationary phases from microscale to nanoscale, we successfully enhance the separation abilities of these "low-performance" MOFs. Three zirconium-based MOFs (NU-1000, PCN-608, and PCN-222) with different organic ligands were synthesized with sizes of tens of micrometers and hundreds of nanometers, respectively. All the nanoscale MOFs exhibited exceedingly higher separation abilities than the respective microscale MOFs. The mechanism investigation proved that reducing the particle size can reduce the mass transfer resistance, thus enhancing the column efficiency by controlling the separation kinetics. Modulating the particle size of MOFs is an efficient way to enhance the separation capability of "low-performance" MOFs and to design high-performance MOF stationary phases.