The inclusion complexes of cucurbitnuril, CBn (n = 6–8), with poly aromatic hydrocarbon (PAH) Benzo(a)Pyrene (BaP), and fluoranthene (FLT) were investigated carefully in aqueous media. Fluorescence and sup.1H NMR spectroscopy were used to characterize and investigate the inclusion complexes that were prepared in the aqueous media. The most predominant complexes of both guests with hosts were the 1:1 guest: host complexes. Stability constants of 2322 ± 547 Msup.−1, 7281 ± 689 Msup.−1, 3566 ± 473 Msup.−1 were obtained for the complexes of BaP with CB6, CB7, and CB8, respectively. On the other hand, stability constants of 5900.270 ± 326 Msup.−1, 726.87 ± 78 Msup.−1, 3327.059 ± 153 Msup.−1 were obtained for the complexes of FLT with CB6, CB7, and CB8, respectively. Molecular dynamic (MD) simulations were used to study the mode and mechanism of the inclusion process and to monitor the stability of these complexes in aqueous media at an atomistic level. Analysis of MD trajectories has shown that both BaP and FLT form stable inclusion complexes with CB7 and CB8 in aqueous media throughout the simulation time, subsequently corroborating the experimental results. Nevertheless, the small size of CB6 prohibited the encapsulation of the two PAHs inside the cavity, but stable exclusion complex was observed between them. The main driving forces for the stability of these complexes are the hydrophobic forces, van der Waals interactions, electrostatic effect, the π····π and C–H···π interaction. These results suggest that BaP and FLT can form stable complexes with CBn (n = 6–8) in solution.