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This work presents a new look at the application of cyclodextrins (CD) as a drug nanocarrier. Two different cyclodextrins (<i>α</i>CD, <i>β</i>CD) were covalently conjugated to branched polyethylenimine (PEI), which was additionally functionalized with folic acid (PEI-<i>β</i>CD-<i>α</i>CD-FA). Here, we demonstrated that the combination of <i>α</i>CD and <i>β</i>CD enabled to load and control release of two anticancer drugs: doxorubicin (DOX) and beta-lapachone (beta-LP) (DOX in <i>β</i>-CD and beta-LP into <i>α</i>-CD) via host-guest inclusion. The PEI-<i>β</i>CD(DOX)-<i>α</i>CD-FA nanoconjugate was used to transport anticancer drugs into A549 lung cancer cells for estimation the cytotoxic and antitumor effect of this nanoconjugate. The presence of FA molecules should facilitate the penetration of studied nanoconjugate into the cell. Whereas, the non-cellular experiments proved that the drugs are released from the carrier mainly in the pH 4.0. The release mechanism is found to be anomalous in all studied cases.