Isostructural metal–organic frameworks (MOFs) MIL-100(Fe) and MIL-100(Cr), which have identical organic linker and Mobil Thirty-Nine zeolitic type, but different metal ions, were exploited as stationary phases for capillary gas chromatographic separation of alkane isomers. MIL-100(Fe) coated capillary column showed great capability and high efficiency for the gas chromatographic separation of alkane isomers without the need of temperature-programming, while MIL-100(Cr) coated capillary column gave poor performance for the separation. The separation performance of MIL-100(Fe) coated capillary column was even better than commercial HP-5MS and GS-GasPro capillary columns. The determined McReynolds constants, adsorption enthalpies and entropies showed that MIL-100(Fe) coated capillary column gave relatively weaker interaction with alkane isomers than MIL-100(Cr) coated capillary column. The relative standard deviations of repeatability for C7 alkane isomers on MIL-100(Fe) coated capillary column were 0.06–0.16%, 1.1–1.5%, 2.8–3.0% and 2.1–2.4% for retention time, half peak width, peak height and peak area, respectively.