This article explores the organization and interactions of Disperse Orange 3 (DO3) hydrophobic dye molecules within hybrid organic-inorganic imogolite nanotubes. In pure water, the DO3 dye molecules self assemble into large insoluble 2D nanosheet whose structure is also explored by molecular dynamic simulations. The dye molecules are however efficiently solubilized when in presence of hybrid imogolite nanotubes. The filling of the internal hydrophobic cavity of the nanotubes is quantified. The organization of the molecules inside the nanotube is probed by the polarization resolved Second Harmonic Scattering (SHS) technique coupled with simulation. At the highest loading, the dyes fill the nanotube with their principal axis parallel to the nanotube walls showing a strong SHS signal due to this encapsulation.