Carboxyethylester-polyrotaxanes (CEE-polyrotaxanes) with the various number of CEE-modified alpha-cyclodextrins (CEE-alpha-CDs) were synthesized, and the effects of the number of CEE-alpha-CDs on calcium binding and trypsin inhibition were investigated. Calcium binding affinity was dependent on the density of the CEE groups accompanied with the number of alpha-CD threading in the CEE-polyrotaxanes. The high number of CEE-alpha-CDs leads to greater inhibition of trypsin activity than poly(acrylic acid), which is mainly due to the good calcium binding affinity. The CEE-polyrotaxane with the smallest number of CEE-alpha-CDs temporally interacted with trypsin, which was well correlated with the inhibition and recovery of trypsin activity. Therefore, the number of CEE-alpha-CDs in the CEE-polyrotaxanes can control the inhibition mechanism of trypsin activity.