Babesia microti is a zoonotic pathogen that mainly parasitizes mammalian erythrocytes. Oxidative stress can induce gene mutation, protein denaturation and lipid peroxidation, such as reactive oxygen species (ROS) induced by hypoxic environment and the host immune system. An antioxidase, B. microti thioredoxin reductase (Bmi TrxR), has been identified in B. microti. We used a combination of homology modeling and domain prediction to explore the functional sites of Bmi TrxR and found that TrxR has three domains. Constructed a mutant pool which His-tag were at the N-terminus (TrxR-Nhis, C105-Nhis, C110-Nhis, C105110-Nhis, C547-Nhis, C552-Nhis, C547552-Nhis) and the His tag were at the N- and C-terminus (TrxR-NChis, C547-NChis, C552-NChis, C547552-NChis). The proteins were expressed as His-tagged fusion proteins in Escherichia coli. The His-tag of TrxR C-terminus were affected the reaction with Trx. The inhibitory efficiency of DNCB was decreased for mutant C547, compared with recombinant TrxR, indicating that the action site of DNCB might be cysteine at position 547. These results indicate that the N-terminal active site of Bmi TrxR plays an important role in accepting electrons and promotes electron transfer. The C-terminus His tag of Bmi TrxR affected the electron transfer and the reducing activity of Bmi TrxR. Reduce reactive oxygen produced in oxidative stress was reduced by Bmi TrxR, which is beneficial to Babesia survival. Therefore, reduction site of TrxR may become a potential target for Babesia microti treatment.