Most of the rod-like liquid crystal compounds (calamitic mesogens), which often exhibit orthogonal smectic phases (SmA, SmB, SmE), have not only a rigid core moiety but also flexible alkyl-chain(s). Although the calamitic mesogens have been investigated for a long time, the roles of the alkyl chain in the orthogonal smectic phases have not been clarified. Here, the importance of alkyl-chain in liquid crystal phases are reviewed. The alkyl-chain is already fully molten even in the SmE phase by the same degree as isotropic liquids, leading to stability of liquid crystal phases. The orientation of the conformationally disordered alkyl-chain yields two types of molecular packing structures in the orthogonal smectic phases. It is demonstrated that the molecular packing structures of the SmA phase correlate closely with the thermodynamic order of the phase transitions between the SmA and nematic phases.