For analytes involved in dynamic equilibrium processes, capillary electrophoresis is a powerful method of determining binding constants. In this work, the complex formation between cucurbit[n]uril (CB[n] n = 6, 7) and some amino compounds was studied by capillary electrophoresis in aqueous formic acid (65% v/v). Four groups of positional and structural isomers (o, m, p-methylanilines; m, p-nitroanilines; benzidine and o-tolidine; alpha, beta-naphthylamines and 1,5-diaminonaphthalene) were selected as model compounds for study of their host-guest inclusion complexation. The interactions between CB[n] (n = 6, 7) and the model compounds were also investigated using a molecular modeling method. The results indicate that the interactions of the compounds with CB[n] (n = 6, 7) are strongly affected by the position of the substituent(s) on the aromatic ring and the ion-dipole interaction between guest molecule and CB. Furthermore, the type and the concentration of CBs on the separation and migration behavior of the amino compounds were also studied.