In this study, we sought to control the assembly of an endotoxin known as the biologically supramolecular lipopolysaccharide (LPS, which consists of three portions: an O antigen, a core carbohydrate, and a lipid A molecule) in order to modulate immunological responses in a manner that has the potential for utilization in vaccine development. Changing the structures of LPS aggregates from lamellas to specific nonlamellas (i.e., cubosomes and hexosomes) can dramatically enhance the strength of LPS in causing inflammatory responses, leading to highly active responses. In order to control the formation of cubosome-free and hexosome-free nonlamellas, we designed a simple strategy based on the use of hydrophilic gold nanodots (AuNDs) to control LPS assembly to facilitate the formation of stable endotoxin nanovesicles, which are stable precursors of cubosomes and hexosomes with specific immunological effects. Structurally, the wall thicknesses of these nanovesicles are exactly twice the lengths of a single LPS molecule, indicating that the LPS molecules adopt a tail-to-tail arrangement (with the lipid A portions acting as the tail domain). The involvement of the hydrophilic AuNDs to laterally link polar domains of LPS can result in the progressive extension of an endotoxically active zone of lipid A assembly, leading to the eventual formation of large-size nanovesicles. Our results showed that endotoxin nanovesicles with such dense lipid A units can elicit the stronger inflammatory gene expressions, including interleukin 6 (IL-6), IL-1A, TNF-α, C-X-C chemokine ligand (CXCL) 1, 2, and 11, which have characteristics of T-helper 1 adjuvants. These findings provide evidence that the concept of manipulating the surface hydrophilicity of AuNDs to control LPS assembly in order to avoid the formation of highly active cubosomes and hexosomes, and thereby modulate immunological responses appropriately, could prove useful in vaccine development.