Molecular dynamics (MD) simulations in aqueous solution were performed for hexameric nanocubes of methylated (1(6)) and demethylated (2(6)) gear-shaped amphiphiles. To elucidate the difference between these nanocubes, the principal component analysis for the MD simulation results in aqueous solution and the normal mode analysis in the gas phase were also applied to the nanocube, 1(6) and 2(6). The structural fluctuation of the lowest-frequency motion on 2(6) is larger than that on 1(6) around the triple it stacking of 3-pyridyl groups. For the structural stability and fluctuation of the nanocube, interactions among the constituent gear-shaped molecules play more important roles than the solvophobic effect due to solvent molecules.