Lipid nanoparticles (LNPs), comprising ionizable lipids, helper lipids, cholesterol, and PEG lipids, can act as delivery carriers for nucleic acids and have achieved clinical success in the delivery of siRNA and mRNA. It has been shown that the morphology of LNPs varies depending on their lipid composition, but the influence of their morphology on nucleic acid efficacy has not been fully elucidated. In this study, we used our previously developed novel lipid, dioleoylglycerophosphate-diethylenediamine conjugate (DOP-DEDA), to create pH-responsive LNPs (DOP-DEDA LNPs). We evaluated the morphology of DOP-DEDA LNPs composed of different helper lipids and the knockdown efficiency of small interfering RNA (siRNA). A distinctive difference in morphology was observed between DOP-DEDA LNPs of different helper lipids. Significant differences were also observed in the apparent pKa of DOP-DEDA LNPs and the knockdown efficiency of siRNA, which may be due to the difference in the localization of DOP-DEDA molecules in DOP-DEDA LNPs. These findings suggest that changing helper lipids alters the morphology of the DOP-DEDA LNP system, which affects the apparent pKa and knockdown efficiency of siRNA.