Thermosonic flip chip bonding is an important technology for the electronic packaging due to its simplicity, cost effectiveness and clean and dry process. Mechanical properties of the horn and the shank, such as the natural frequency and the amplitude, have a great effect on the bonding capability of the transverse flip chip bonding system. In this study, an endeavor has been made to design the horn and shank as an assembly. A commercial FEM software (ANSYS) is used to analyze the system. New design of the clamp to hold the horn at the nodal point is also introduced. The clamp with a bent shape is newly designed. It shows the ability to increase the amplitude of the vibration at the end of the horn compared with the straight-cylindrical-type-clamp.For the optimal design of the horn-shank assembly system, it is studied the effect of the design parameters and the tolerance on the vibration amplitude and planarity at the end of the shank. The variation of the design parameters and the tolerance changes the amplitude and the frequency of the vibration of the shank. They, in turn, have an effect on the quantity of the plastic deformation of the gold ball bump, which determined the quality of the flip chip bonding. The design and tolerance parameters that give the great effect on the amplitude of the shank are determined using Taguchi's method. Error of set-up angle, the length and diameter of horn and error of the length of the shank are determined to be the parameters that have great effect on the amplitude of the system.