The development of novel systems for chiral polyoxometalates (POMs) is an attractive research field because of their fascinating topological structures and well-defined functions. Herein, we have developed a new reaction route for the synthesis of two unprecedented chiral Waugh POM-based supramolecular architectures. Single-crystal X-ray diffraction reveals that the architectures exhibit a wavy three-dimensional framework and bamboo-rod-connected framework upon regulating the size of the cyclodextrin and the stacking pattern of the D3 symmetric Waugh {MnMo9}. Solution studies using NMR, circular dichroism and isothermal titration calorimetry corroborate nicely the very weak interactions between the components. The intricate chiral microenvironment originating from the hybrid frameworks may be responsible for the selective recognition of the Λ-{MnMo9} enantiomer. This study highlights the importance of the asymmetric configuration of the POM for designing CD/POM assemblies and understanding their chirality.