Molecular dynamics (MD) simulation was carried out for an antiferroelectric liquid crystalline molecule, (S)-4-[(1-methylheptyloxycarbonyl]phenyl 4'-octyloxybiphenyl-4'-carboxylate (MHPOBC), to analyze its conformational property in smectic liquid crystalline phases. The MD simulation reproduces a "solid-SmC(x)-SmA-isotropic" phase transition. The MHPOBC molecules in the SmC(x) phase are packed in a tilted layered structure, while in the SmA phase the molecular tilt disappears. The chiral alkyl chain in the crystalline phase has a larger gauche population at the C*-C bond, which gives rise to a "highly bent structure". In smectic phases, the conformation of both chiral and achiral alkyl chains is almost fully liberated, and the average molecular shape changes into a "moderately bent structure". Comparison of the results of MD simulation and molecular orbital calculation indicates that the smectic phases of MHPOBC can be distinguished from the solid phase in terms of the alkyl chain conformation, and the SmC(x) and SmA phases are distinguished from each other in terms of molecular packing structure.