Extraction mechanisms of charged organic dye molecules are examined for an assembly of silica-surfactant nanochannels with a channel diameter of 3.4 nm, which is formed inside the pores of an anodic alumina membrane by a surfactant-template method. Experimental results confirm that the extraction mechanism depends on the sign of a charge of the dye molecules. The extraction of the cationic rhodamine 6G is predominantly caused by an ion-pair extraction process, whereas an anion-exchange process is mainly responsible for the extraction of the anionic sulforhodamine B. These extraction mechanisms are discussed by considering the microstructures of the silica-surfactant nanochannels.