The purpose of this study is to apply optical waveguide (OWG) spectroscopy to characterize the encapsulation behavior of enzymes modified with polyethylene glycol (PEG), i.e. pegylation, in a hydrophobic mesoporous silica film. For that purpose, pegylated myoglobin (PEG-Mb) was introduced into the silica mesopores modified with octadecylsilyl (ODS) groups and studied by OWG spectroscopy. OWG spectroscopy confirmed that the hydrophobic interaction between the PEG group and the surface ODS group promoted the encapsulation of PEG-Mb into the hydrophobic silica mesopores. The surface density of ODS affected the adsorbed amount of PEG-Mb and the higher surface density of the ODS group resulted in the suppression of adsorption and diffusion of PEG-Mb inside the pore. Since the desorption rate of PEG-Mb was found to be much slower than the adsorption rate, the pegylation of an enzyme could be effective for the enzyme encapsulation into the hydrophobic mesoporous silica host.