A method to control the release of the anti-cancer drug doxorubicin (Dox) from cylindrical nanocapsules, known as organic nanotubes (ONTs), is reported. Co-assembly of a tube-forming glycolipid and its hydrophobized analogue yield novel ONTs with both –COOH and hydrophobic benzyloxycarbonyl groups localized on cylindrical nanochannels. The hydrophobicity of the ONTs nanochannels is easily tunable by adjusting the mixing ratio of the two glycolipids in the co-assembly process. The resultant biologically stable ONTs are able to capture Dox with high efficiency into the cylindrical nanochannels via ion complexation between cationic Dox and anionic –COO−, and the release of Dox from hybrid ONTs is effectively controlled by tuning the electrostatic interaction and the hydrophobicity. This controlled release by tuning the hydrophobicity of the ONTs' nanochannels greatly reduces the cytotoxicity of Dox@ONTs for HeLa cells.