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Direct cytosolic delivery of the Cas9 ribonucleoprotein is the most promising method for inducing CRISPR-Cas9 genome editing in mammalian cells. Recently, we focused the movable properties of cyclodextrin-based polyrotaxanes (PRXs), which consist of numerous cyclodextrins threaded onto the axile molecule with bulky endcaps at both ends of the axile molecule, and developed aminated PRXs as multistep transformable carriers for Cas9 ribonucleoprotein, ensuring efficient complexation, cellular internalization, endosomal escape, release, and nuclear localization. This study reports the structural fine-tuning and structure-property relationship of multistep transformable PRXs for more efficient Cas9 ribonucleoprotein delivery. Among various PRXs, PRX derivatives with a longer molecular length (35 kDa polyethylene glycol as the axile molecule) and a low total degree of substitution (1.5 amino groups/α-cyclodextrins), as well as the modified ratio of two modified amines (cystamine and diethylenetriamine) = ≈1:1, exhibited the highest genome-editing efficacy and intracellular dynamics control. These structural properties are important for efficient endosomal escape and Cas9 RNP release. Furthermore, ligand-modified-β-CD, which can endow the ligand through complexation with PRX termini, improved the cellular uptake and genome-editing effects of the optimized PRX/Cas9 RNP in target cells. Thus, structural fine-tuning and the addition of ligand-modified-β-cyclodextrin enabled efficient genome editing by the Cas9 RNP. [Display omitted] [ABSTRACT FROM AUTHOR]