In the present study, we correlated for the first time, the molecular chiral structure of a phospholipid (dipalmitoylphosphatidylcholine; DPPC) and the handedness of the mesoscopic domain composed of DPPC using an effective pair potential (EPP) theory. The study uses a coarse-grained description of the molecule and calculates the pair potential between a pair of molecules without using any adjustable parameter. The agreement between the theoretical results and the experimental observations is excellent. In addition to the molecular explanation of the handedness, the study also explains why the distribution of the headgroup orientation in the aqueous subphase does not destroy the chirality of the domain shape. This study explains the influence of chirality at the lower level of structural hierarchy on the chirality at a higher level in biomimetic systems.