A “threading-stoppering-followed-by-clipping” approach was used for the synthesis of a hetero[4]rotaxane, in which one cucurbit[6]uril (CB[6]) and two hetero crown ether macrocycles are threaded onto one dumbbell-shaped molecule. The process involves three steps: (1) threading of a CB[6] macrocycle onto a thread containing two dialkylammonium sites to form a CB[6]-based pseudo[2]rotaxane; (2) stoppering of the as-formed pseudo[2]rotaxane by imine condensation reaction followed by reduction/protonation to afford a CB[6]-based [2]rotaxane with two new dialkylammonium sites; and (3) selective clipping of two hetero crown ether macrocycles onto the newly-formed ammonium sites and subsequent reduction of the imine bonds in each crown ether to afford the final hetero[4]rotaxane in good yield. The whole process was followed by NMR spectroscopy and the structure of the hetero[4]rotaxane was confirmed by NMR spectroscopy, elemental analysis and mass spectrometry.