Cyclodextrin (CD) extraction is widely used for the remediation of polycyclic aromatic hydrocarbons (PAH) pollution, but it remains unclear about the influence of CD aggregation on the PAH transport from non-aqueous liquid phase to water. The atomistic adsorption and complexation of PAHs (32 anthracenes) by CD aggregates (48 beta-cyclodextrins) were studied by molecular dynamics simulations at hundreds of nanoseconds time scale. Results indicated that high temperature promoted the beta CD aggregation in bulk oil, which was not found in bulk water. Nevertheless, the fractions of anthracenes entrapped inside the beta CDs cavity in both scenarios were significantly increased when temperature increased from 298 to 328 K. Free energy calculation for the sub-steps of CD extraction demonstrated that the anthracenes could be extracted when the beta CDs arrived at the water-oil interface or after the beta CDs entered the bulk oil. The former was kinetic-controlled while the latter was thermodynamic-limited process. Results also highlighted the formation of porous structures by CD aggregates in water, which was able to sequestrate PAH clusters with the size obviously larger than the cavity diameter of individual CD. This provided an opportunity for the extraction of recalcitrant PAHs with molecular size larger than anthracenes by cyclodextrins. (C) 2016 Elsevier B.V. All rights reserved.