The phase structures and transition behaviors of a novel liquid crystal compound containing biphenylyl mesogen, 5-{[(4′-heptoxy-4-biphenylyl) oxy]carbonyl}-1-pentyne (A3E′O7), have been investigated by differential scanning calorimetry (DSC), polarizing optical microscopy (POM) and wide angle X-ray diffraction (WAXD). In contrast to the published compound 5-{[(4′-heptoxy-4-biphenyl-yl)carbonyl]oxy}-1-pentyne (A3EO7), in which the ester bridge between the mesogenic core and the flexible spacer has different linkage order, A3E′O7 shows strikingly different phase structure and transition behaviors. Overall, A3E′O7 has better packing order and higher transition temperatures. It undergoes three enantiotropic stable liquid crystalline phases which are associated to smectic A (S A ) phase (100.2–98.2 °C), smectic C (S C ) phase (98.2–87.2 °C) and highly ordered smectic X (S X ) phase (87.2–63.3 °C), respectively, till eventual crystallization takes place upon cooling from isotropic state to room temperature. However, A3EO7 only shows monotropic S A (72.4–53.6 °C) phase and the metastable monotropic S C phase provided that the same thermal treatment is applied. We successfully observed the extremely weak transition of S A to S C by DSC measurement, which is reported to be normally almost undetectable even by using the most sophisticated instrument due to its second-order transition in nature. Additionally, the pronounced mixed liquid crystalline textures observed in A3E′O7 are not common for the liquid crystal compound having low molar mass.