AbstractSelf‐assembled lipid nanoparticles (LNPs), serving as essential nanocarriers in recent COVID‐19 mRNA vaccines, provide a stable and versatile platform for delivering a wide range of biological materials. Notably, LNPs with unique inverse mesostructures, such as cubosomes and hexosomes, are recognized as fusogenic nanocarriers in the drug delivery field. This study delves into the physicochemical properties, including size, lyotropic liquid crystalline mesophase, and apparent pK_a of LNPs with various lipid components, consisting of two ionizable lipids (ALC‐0315 and SM‐102) used in commercial COVID‐19 mRNA vaccines and a well‐known inverse mesophase structure‐forming helper lipid, phytantriol (PT). Two partial mesophase diagrams are generated for both ALC‐0315/PT LNPs and SM‐102/PT LNPs as a function of two factors, ionizable lipid ratio (α, 0–100 mol%) and pH condition (pH 3–11). Furthermore, the impact of different LNP stabilizers (Pluronic F127, Pluronic F108, and Tween 80) on their pH‐dependent phase behavior is evaluated. The findings offer insights into the self‐assembled mesostructure and ionization state of the studied LNPs with potentially enhanced endosomal escape ability. This research is relevant to developing innovative next‐generation LNP systems for delivering various therapeutics.