The interactions between enzyme and nanoparticles (NPs) are governed by the key properties of NPs, such as structure, size, surface chemistry, charge, and surface shape. In this report, we compared the effect of oxidized multiwalled carbon nanotubes (OXWNT) and irradiated multiwalled carbon nanotubes (IRWNT) on the enzymatic activity of PchPipA. Both OXWNT and IRWNT decreased the biocatalytic activity of PchPipA to some extent when they were added in the reaction system, while OXWNT exhibited higher inhibition of the activity of PchPipA than IRWNT. These results suggested that the water solubility may be another property that can affect the interaction of bio-macromolecular products and nanoparticles.