Singlet oxygen (¹O₂) formed through photosensitization may initiate oxidative destruction of biomembranes, however, the influence from the spatial organization of photosensitizers (PS) relative to membranes remains unclear. To clarify this issue, we loaded riboflavin 5′-(dihydrogen phosphate) monosodium (FMN-Na) as a hydrophilic PS into the lumen of halloysite nanotubes (HNTs), and attached the nanoassemblies (FMN-Na@HNTs), via Pickering effects, to the outer surfaces of giant unilamellar vesicles (GUVs) of phospholipids. We also prepared GUVs dopped with lumiflavin (LF) as a lipophilic PS having a ¹O₂ quantum yield comparable to FMN-Na. FMN-Na capsulated in HNT was characterized by a longer triplet excited state lifetime (12.1 μs) compared to FMN-Na free in solution (7.5 μs), and FMN-Na in both forms efficiently generated ¹O₂ upon illumination. The spatio-effects of PS on the photosensitized morphological changes of membranes were studied using conventional optical microscopy by monitoring GUV morphological changes. Upon light exposure (400–440 nm), the GUVs attached with FMN-Na@HNT merely experienced membrane deformation starting from the original spherical shape, ascribed to Type II photosensitization with ¹O₂ as oxidant. In contrast, photooxidation of LF dopped GUVs mainly led to membrane coarsening and budding assigned to Type I photosensitization. The spatial effects of PS on photosensitized morphological changes were related to the different lipid oxidation products generated through Type I and Type II photosensitized lipid oxidation.