Three series of amphiphilic mesogens containing a cyanostilbene core with zero, one or two lateral fluorine atoms, which attach one polar glycerol group at one end and three lipophilic alkyl chains at the other end were synthesized by Suzuki coupling and Knoevenagel reactions. The thermodynamics, liquid crystalline and photophysical properties of these amphiphilic mesogens were evaluated by polarized optical microscopy, differential scanning calorimetry, small-angle X-ray diffraction, density functional theory calculation, absorption and emission spectra. The non-fluoro and mono-fluoro amphiphilic mesogens display a mesophase transition from hexagonal columnar phase to three-dimensional micellar cubic phase with Im3¯m lattice by the increase of temperature or the elongation of terminal lipophilic alkyl chains. The bi-fluoro amphiphilic mesogens can only self-organize into hexagonal columnar mesophase. Similar spectral properties and weak solvatochromism in these amphiphilic mesogens are observed attributed to the weak intramolecular charge transfer and weak influence of fluorine atom on the electronic properties in both ground and excited states. In addition, aggregation-induced emission behavior could be achieved in these amphiphilic mesogens due to the twisted molecular configuration. Therefore, complex self-assembly structures and interesting photophysical properties may be altered by varying the degree of fluorination of amphiphilic mesogens, which could promote the application of liquid crystalline materials.