In this paper, two new amino acid imidazole ionic liquids IL‐3 and IL‐4 were synthesized for the first time, and their separation performance as the stationary phase for capillary gas chromatography (GC) was tested. The statically coated IL‐3 and IL‐4 capillary columns exhibited moderate to high polarity, and achieved the column efficiency of 2242 plates/m and 2487 plates/m respectively determined by n‐octanol at 120 °C. Importantly, the IL‐3 and IL‐4 columns exhibited excellent separation capability for analytes with varying polarity, including n‐alkanes, arenes, esters, alcohols, bromoalkanes, halogenobenzenes, and halogenated anilines. In addition, the IL‐3 and IL‐4 columns presented high selectivity and separation capability for positional, structural and cis‐/trans‐isomers. In particular, they showed high separation performance of the chloroaniline, bromaniline, iodoaniline and xylidine isomers as an important environmental pollutant. The IL‐3 and IL‐4 columns displayed advantageous resolving capability over the commercial HP‐35 column for aromatic amine isomers, and the separation performance of IL‐4 with long carbon chain was better than that of IL‐3. Moreover, it was applied to determine isomer impurities in real samples, and showing huge potential in GC applications. This work demonstrates the potential of the amino acid imidazole ionic liquids as a new type of stationary phase in GC separations.