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Cationic azole-based metal-organic frameworks (MOFs) with remarkable stability and unique pore environment have aroused great research interests. Meanwhile, flexible MOFs which can undergo pore-structure changes upon exposure to external stimuli are ideal materials for gas separation. However, introducing flexibility into the framework of cationic azole-based MOFs is rarely reported. Herein, we synthesized two stable isomorphic cationic MOFs (M-btz-as, M = Co, Ni) based on a linear azole ligand. After activated at high temperature under vacuum, M-btz-ht (M = Co, Ni) were obtained and both MOFs exhibited flexible features in which Co-btz is more flexible than Ni-btz. Different solvent-mediated activation methods were employed to explore their effects on structural flexibility and produced MOFs with different phases. Continuous phase transformation of Co-btz-e was verified by powder X-ray diffraction. In addition, these MOF phases possessed different gas separation abilities affected by their flexible frameworks, and Co-btz-ht exhibited the highest CO2/CH4 separation ability.