We examined the lateral packing structure of intercellular lipids (ICL) in the lip stratum corneum (SC) by low-flux electron diffraction (LFED) to obtain new insights into the causes of high transepidermal water loss (TEWL) and low water retention, which may increase the vulnerability of the lip to chapping. Similar to skin SC-ICLs, we found coexistence of orthorhombic and hexagonal phases in lip SC-ICLs. We also found that electron diffraction (ED) images with no sharp peaks and a relatively small broad peak at around 2.2 nm−1 appeared frequently, unlike skin SC-ICLs. This suggests that a large fraction of corneocytes in the lip SC is surrounded by thin ICL layers in the fluid phase. Such structural features of lip SC-ICLs can explain its inferior barrier function. Furthermore, we calculated the frequency of appearance of ED images with no sharp peaks, Af, and quantitatively analyzed its correlation with water content and TEWL. The analysis showed a negative correlation between Af and water content when Af > 50%. This is the first report on the detailed analysis of lipid organization in lip SC-ICLs and showed that the LFED method in combination with quasi-noninvasive sample collection by the grid-stripping technique is useful for statistical study of the fine structures in lip SC and is a promising approach for obtaining clues to the structural factors regulating the water content and TEWL in lip SC, leading to more effective lip care products.