We synthesized [2]rotaxanes featuring a catechol borate ion-containing crown ether and secondary ammonium ions. These rotaxane components show both ion-ion interactions and hydrogen bonds. X-ray crystallography and NMR spectroscopy allowed elucidation of the rotaxane structure. Moreover, 1H NMR spectroscopy revealed the rotaxane synthesis can be thermodynamically controlled. The binding affinity between the borate-containing crown ether and ammonium ions is enhanced by ion-pairing.