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The supramolecular interaction of anthracene (ANT) and phenanthrene (PHN) with cucurbit[n]uril, CB[n] (n=6‐8) has been investigated in aqueous media for the first time. The inclusion complexes were investigated and characterized by fluorescence spectroscopy, matrix‐assisted laser desorption ionization time‐of‐flight (MALDI‐TOF) mass spectrometry, and 1HNMR. The stability of these complexes and the mode of inclusion in aqueous media at atomistic levels were monitored by molecular dynamic (MD) simulations. The results obtained from the experimental and MD studies have demonstrated the formation of stable 1 : 1 complexes between the two guests with all hosts in aqueous media. From the fluorescence study, the binding constants of PHN with CB[6], CB[7], and CB[8] were found to be 398±63, 544±128, and 655±162 M−1, respectively. Whereas, ANT‐ CB[n] formation constants are 213±37 M−1 270±35 M−1, and 356±94 M−1 for CB[6], CB[7], and CB[8], respectively. The results obtained show that the size of the cavity of the macrocycle and the polarity of the rim play an important role in the stability of the formed complex. Surprisingly, CB[6] forms an inclusion complex with ANT while it interacts by its side with PHN through dipole‐dipole interaction. The larger cavity sizes of CB[7], CB[8], were found to encapsulate the two guests forming highly stable inclusion complexes. [ABSTRACT FROM AUTHOR]