A method has been proposed for the formation of self-organized ensembles of carbon nanotubes with the use of coordinating cumene molecules and the development of secondary porosity in the obtained structures. It has been shown that the fraction of nanotubes coordinated into an array grows with increasing molar ratio between cumene molecules and carbon nanotubes upon the synthesis of the supramolecular structures. The secondary porosity develops due to partial desorption of the coordinating molecules from the obtained structure. A supramolecular structure with a residual cumene content of 50 wt % possesses the best adsorption characteristics for the described system. Specific adsorption of nitrogen on the “carbon nanotubes–cumene (50 wt %)” supramolecular structure at 293 K is more than an order of magnitude higher than that on the initial nanotubes. The structure-related energy parameters of the experimentally obtained supramolecular systems have been determined by molecular dynamics methods. The calculation in terms of the theory of volume filling of micropores has shown that the secondary pores of the obtained structures can accumulate methane and hydrogen in amounts as large as 213 nm3/m3 and 4 wt %, respectively.