The structure of copper(II) bis(1-phenyl-3-methyl-4-dodecyliminomethylenepyrazol-5-onate) CuL2 (I) at room temperature has been determined by X-ray crystallography. DSC study has shown that compound I undergoes a solid-phase low-temperature transition (T = −28°C) to modification II (its structure has been determined previously). The structures of both modifications are composed of complex molecules combined by π-π stacking into molecular dimers (MDs) which, being in close contact with adjacent MDs, form planar layers one MD thick. These layers remain unaltered during the phase transition. The essence of the transition is in that one of the two CH2)11(CH3)3 groups of the Cu complex at room temperature is in the “molten” state, which stimulates the rearrangement of the aliphatic zone of the crystal. As temperature changes, channels with potentially increased mobility of atoms are formed in the aliphatic zone. According to the concepts of supramolecular chemistry, the morphotropic transition occurs through a simple rotation by ±45° of the aliphatic moiety of the supramolecular assembly in the “nematic” CuL2 crystal.