The high specificity and sustainability of enzymes make them widely used as green catalysts, and their stability and catalytic activity are vital for their practical applicability. Recently, enzymes have been endowed with desired physical and catalytic properties via using protein structural modification. From the protein structural point of view, enzyme thermal stability has been improved by modulation of non-covalent/covalent interactions (hydrophobic interaction, hydrogen bonding, salt bridges, aromatic interaction and disulfide bonds), loop truncation, C-/N-terminal engineering, introduction of proline with highest conformational rigidity in the flexible region, and substitution of glycine with highest conformational entropy. Meanwhile, the catalytic function has been enhanced or altered by various methods, including reducing steric hindrance, widening the binding pocket, moderating substrate binding affinity and active site flexibility. While, the generation of new features or improvement of the existing features often comes at the expense of the other ones. Thus, strategies include screening suitable mutation sites, co-selection for stability and activity, and using highly stable proteins as the parental backbones are also discussed to overcome the stability-activity trade-off. This review summarized recent advances in structural modification to improve the stability or/and catalytic activity of enzymes and further provided a brief prospect in the future developments.