Halloysite nanotube (HNT) is a natural bio-compatible and stable nanomaterial available in abundance at low-cost. In this work, HNT was modified by two strategies to make it suitable for supporting immobilization of chloroperoxidase (CPO). Firstly, FeO nanoparticles were deposited on HNT, so magnetic separation can be used instead of centrifugation. Then, the magnetic HNT was modified by 3-aminopropyltriethoxysilane (APTES), which can provide amine group on surface of HNT and meanwhile inhibit the agglomeration of magnetic HNT. Then, HNT-FeO -APTES was linked with branched polyethyleneimine (PEI) to provide more amino for binding with enzyme. The so-prepared CPO@HNT-FeO-APTES-PEI showed enhanced enzyme loading, reusability, improved thermal stability and tolerance to organic solvents than free CPO. For example, after 10 repeated uses, CPO@HNT- FeO-APTES-PEI can maintain 92.20% of its original activity compared with 65.12% of activity of CPO@HNT-APTES-PEI and 45.69% of activity of CPO@HNT. The kinetic parameters indicated the affinity and specificity of immobilized enzyme to substrate was increased. CPO@HNT-FeO-APTES-PEI was very efficient when it was applied in the degradation of pesticides mesotrione in wastewater. The degradation efficiency can reach 90% within 20 min at range of 5-40 μmol·L. These results ensure the potential practical application of this bio-materials in wastewater treatment.