The development of novel biodegradable supermolecules is of importance in designing functionalized biomaterials utilized in the field of tissue engineering and drug delivery. In this regard, the focus here is on biocompatible and biodegradable polyphosphoester ionomers, and their pseudopolyrotaxane (PPRX) formation with α‐, β‐, or γ‐cyclodextrins (CDs) is examined. Poly(2‐hydroxy‐2‐oxo‐1,3,2‐dioxaphosphorane) (PHP) is found to form a precipitate upon mixing with α‐CD in water. Also, precipitation is observed by mixing PHP and γ‐CD, although its yield is lower than with α‐CD. The stoichiometry ratio of PHP monomer unit:α‐CD is determined to be 1:1 from the 1H NMR spectra of the precipitate. The wide‐angle X‐ray diffraction pattern of the precipitate between PHP and α‐CD clearly supports the formation of PPRX, and its crystalline structure is well consistent with previously reported α‐CD‐based PPRXs. This finding contributes to the design of novel supramolecular biomaterials.