Bolt stiffness and pre-tightening force have great impact on structural modal and transfer function, which are often ignored in the actual assembling because of the difficult processing. By comparing the finite element calculation data and test data of three kinds of bolts with different stiffness under different pre-tightening force, changes of structure modal and transfer function are analyzed. First simulation analysis and calculation are made by ANSYS software pre-stressed modal and harmonic response. Then the tests of three kinds of bolts with different stiffness bolts are done under the same pre-tightening force, and the steel bolt is tested under six groups of pre-tightening force. Finally, the differences between calculation data and test data are studied. The study results show that the calculation value differs about 15% from test data because the contact damping is ignored. Under the same pre-tightening force, the natural frequency is increasing with the increasing of the bolt stiffness, but the maximum distortion also increases. The structure transfer function will be easier to find as the pre-tightening force increasing.