We report a new class of liquid crystalline system exhibiting columnar mesophases, which are constructed by the hierarchical supramolecular self-organization of a rod-like diacetylene derivative as the primary building block. A series of 1,3-alkadiynyl-4-benzoic acids (mmDA) with different alkyl chain lengths (m = 8–16) were synthesized and their mesophase properties were investigated by differential scanning calorimetry, polarized optical microscopy, and X-ray diffraction under temperature control. The mmDA exhibited three types of mesophases, i.e., a discotic lamellar phase, DL, and two columnar rectangular phases, Colrd and Colro, with disordered and ordered stacking structures of the mesogens in a column, respectively, depending on the length of the alkyl substituent and temperature. We have revealed that the columnar mesophase structures are constructed with the rod-like mmDA molecules as the starting building blocks by hierarchical self-organization. The hydrogen-bonded dimers of the carboxylic acid with a rigid framework are assembled to provide a disc-like mesogen unit, which consists of a π-stacked core-part and peripheral alkyl-chains. The discotic supramolecular mesogens further stack in ordered and disordered columnar structures, producing the Colro and Colrd mesophases, or in the layer DL mesophase. This is a rare example for the discotic mesophases using the rod-like diacetylenes with a non-branched molecular structure.