Abstract The targeted or responsive systems are appealing therapeutic platforms for the development of next-generation precision medications. In this article the first experimental and theoretical investigation of the complexation between podophyllotoxin (POD) and three β-cyclodextrin (β-CD) derivatives (NH2-β-CD, SA-β-CD and Bridged β-CD) are presented. The inclusion complexes are characterized by 1H and 2D nuclear magnetic resonance (NMR), thermal gravimetric analysis (TGA), and X-ray powder diffraction (XRD). Cytotoxicity tests are furnished by MTT assay. The results show that POD is encapsulated in the cavity of β-CD derivatives to form inclusion complexes with different stability constants (Ks). The cytotoxicity of these inclusion complexes against normal human kidney cell line 293 T is significantly reduced, while the inclusion complexes of SA-β-CD/POD and Bridged-β-CD/POD exhibit the same cytotoxicity against cancerous cell lines HCT116, HepG2 and SY5Y in comparison with native POD. Moreover, the stability constants of the inclusion complexes can affect their cytotoxicity, which provides a strategy for low cytotoxicity systems of POD for clinical application.