Cross-linked enzyme aggregates (CLEAs) have emerged as an interesting biocatalyst design for enzyme immobilization. However, the commercialization of CLEAs is often hampered by their shortcomings, such as poor controlled particle size, low activity and sticky characteristic. In order to overcome these drawbacks, five nanoparticles (NPs) (nano-TiO2, nano-MgO, nano-Ni, nano-Cu and nano-Fe3O4) were used to improve CLEAs activity and structure in this study. Results showed that moderate dosage of nano-TiO2 addition increased CLEAs activity, and the most increment was 15.2% relative to CLEAs without NPs. This was possibly due to more channels and smaller size particle of CLEAs after nano-TiO2 addition. Moreover, nano-TiO2 addition not only decreased fluorescence intensity but also caused the red shift in tryptophan (Trp) and tyrosine (Typ) residues. Nano-TiO2 addition decreased Km and increased Vmax of CLEAs. These changes were benefit to the activity and structure of CLEAs. However, addition of other four NPs (nano-MgO, nano-Ni, nano-Cu and nano-Fe3O4) did not increase CLEAs activity and even decrease CLEAs activity due to less amorphous cavities and larger or discrete particle size than CLEAs without NPs. In addition, PT-IR results showed that NPs addition increases the content of regular structure of CLEAs, and causes a partial transformation of 13-turn into 13-sheet. This study showed that it was potential to improve CLEAs performance by nano-Tio(2) addition.