Noncovalent interaction of methylene blue dye cation (MB⁺) with single walled carbon nanotubes (CNT) is characterized by molecular dynamics (MD) simulation, quantum chemical calculations, and laser desorption/ionization (LDI) mass spectrometry. The MD simulation of the (MB⁺)_n–CNT (n = 1–10) complexes in water demonstrates that the MB⁺ cations are adsorbed on the nanotube surface in the monomeric form. MD reveals both parallel and perpendicular orientations of the MB⁺ tricyclic plane in relation to the long axis of CNT when placed in the water environment. The interaction energy between the components of the complex in the perpendicular conformation, as determined by quantum chemical calculations at the DFT/M05-2X/6-31++G(d,p) level of theory, explains why the bending of the MB⁺ cation at the sulfur atom weakens the π-system of bonds and allows for the perpendicular orientation to occur. It is also found that the adsorbed MB⁺ induces positive electrostatic potential around the adjacent semicylindrical segment of the nanotube. The mainly monomolecular adsorption of the MB⁺ cations at the CNT surface leads to the absence in the LDI mass spectra of (MB⁺)_n–CNT of features corresponding to products of the reduction of MB⁺ commonly observed in the LDI mass spectra of crystalline dyes.