Promoting fluid transportation in porous media has important applications in energy, pedology, bioscience, etc. For this purpose, one effective way is to prevent swelling through surface modification; however, it is far from enough in real cases, such as ultra-low permeability reservoirs and tight oils. In this study, we considered the comprehensive effects of inhibiting clay swelling, flocculation performance, reducing water clusters and interfacial tension and developed a series of imidazole-based tetrafluoroborate ionic liquids (ILs) with different lengths of alkyl chains. Through measurements of anti-swelling rates, XRD, SEM, 17O NMR, molecular dynamics simulation, zeta potential, flocculation evaluation, interfacial tension and a core flooding experiment based on ultra-low permeability reservoirs, the relationships between the molecular structure and physicochemical properties of ILs have been revealed. Interestingly, one of the selected ILs, imidazole-based tetrafluoroborate ILs (C8-OMImBF4), shows excellent performance, which is helpful to design an effective strategy in promoting fluid transportation in narrow spaces.