Two reversible trypsin inhibitors, Kunitz trypsin inhibitor (KTI) and Bowman-Birk trypsin inhibitor (BBI) were compared to find the more optimal one as the inhibit factor during trypsin immobilization. Fluorescence spectroscopy, UV–visible absorption spectroscopy and circular dichroism (CD) spectroscopy were used to explore the effects of the two inhibitors on trypsin in activity and structure. The results showed that both inhibitors combined with trypsin in 1:1. CD circular dichroism spectroscopy showed that KTI and BBI led to different changes in trypsin second structure. The results can help us find out the mechanism between the two inhibitors and trypsin and select the more optimal inhibitor in trypsin immobilization.