A series of linear polyethylenimines (LPEIs) with various molecular weights were synthesized and used for pH-dependent polypseudorotaxane formation with alpha- or gamma-cyclodextrins (alpha-, gamma-CDs). The polypseudorotaxane formation was significantly dependent on the pH of the aqueous media. The maximum yield of the recovered polypseudorotaxane precipitates was observed at pH 11.0, whereas no complexation was observed in the pH range below 8.0 due to the protonation of secondary amine groups in LPEI backbones. This suggests that the ionization of the secondary amine groups leads to dethreading of CD molecules because PEI chains with cationic nature disfavor the hydrophobic cavities of CDs. The solid-state C-13 CP/MAS NMR and X-ray diffraction measurements verified the successful formation of crystalline polypseudorotaxanes through the inclusion complexation. In addition, H-1 NMR analysis showed that LPEI formed a 2:1 inclusion complex with alpha-CD ([EI]:[alpha-CD] = 2:1) and a 4:1 complex with gamma-CD ([EI]: [gamma-CD] = 4: 1) as reported in the poly(ethylene glycol)-based polypseudorotaxane system. Such unique pH-controllable polypseudorotaxane formation may be useful in designing many building blocks for stimuli-responsive polyrotaxanes.