Optimizing the balance between thermodynamic interaction and kinetic diffusion is pivotal to obtaining high-performance gas chromatographic stationary phases. Here, three aluminum-based metal-organic frameworks featuring fym topology were chosen to achieve such balance by refined controlling the thermodynamic interactions toward analytes at angstrom level in a confined space. The CAU-10-H with the middle-sized channels (5.4 Å) provided weak interactions with xylenes because of the benzene ring around the channel, leading to the fastest diffusion. While the MIL-160 provided stronger interactions toward the analytes due to the abundance of O-heterocyclic sites of 2,5-furandicarboxylic acid ligands, resulting in slightly higher diffusion barriers. Thereby, although MIL-160 had a larger channel (5.9 Å) than CAU-10-H, the xylenes still diffused more slowly in MIL-160 than in CAU-10-H. The CAU-10-NH2 with the channel of 4.7 Å provided overstrong thermodynamic interactions and significant stereospecific blockade to the analytes because of the NH2 sites in the confined channels. These factors collectively contributed to achieving the lowest diffusion kinetics. The confined interactions were also proved by molecular dynamics simulation. Furthermore, the application indicated that MIL-160 exhibited the highest separation ability as a GC stationary phase among all reported materials. This strategy offers an approach for developing high-performance MOF stationary phases.