Fusion protein IIn-UK was constructed by fusing ScFv specific against human fibrin with low molecular urokinase with linker (G₄S)₃, and this fusion protein was a potential targeting thrombolytic agent. But the fusion protein leaned to be proteolysed while expressed in CHO cells. To overcome this problem, four new linkers were selected from linkers database by using the program at http://ibivu.cs.vu.nl /programs/ linkerdbwww, and four IIn-UK fusion genes were reconstructed by replacing linkers. And other four fusion genes were reconstructed by changing reletive position of two moities and replacing the linker. The degree of proteolysis of eight reconstructed IIn-linker-UK or UK-linker-IIn fusion proteins were analysed with Western blot by using anti-urokinase antibody, the results showed that all eight constructed fusion proteins were degraded partly while expressed in CHO cells. So three new IIn-linker UK fusion genes were constructed by using a new linker coming from pro-urokinase and removing one or two cleavage site of proteolytic enzyme around the linker. The Western blot showed that IIn-UK fusion protein removed two protyolitic enzyme cleavage sites had good anti-proteolysis ability in COS7 cell and CHO cell. Thus it laid a foundation for preparation of IIn-UK fusion protein in CHO cells and further research of targeting thrombolytic agent.