A series of purely organic macrocycles and catenanes can be self-assembled by condensing a cationic bisaldehyde compound with a series of dihydrazide linkers in weakly acidic water. On one hand, the macrocycles could be generated as the predominant products under the condition of low concentration or less polar media. In the presence of a guest template, these macrocycles could even be obtained in close to quantitative yields, allowing them to be isolated as pure solid products without the need for chromatographic purification. On the other hand, [2]catenanes could be obtained as the major products in more concentrated solutions or more polar media where hydrophobic effects are enhanced. Once purified, both macrocycles and catenanes exhibit remarkable kinetic stability in both the solid state and neutral aqueous solution at room temperature. By means of selective host-guest recognition, one of the macrocyclic products is capable of resolving a pair of hydrocarbon isomers, namely phenanthrene and anthracene, which have similar properties and can hardly be separated by commonly used approaches.