This paper proposes a method to evaluate the deformation of the bonding tool and executes experiments to verify the evaluated results. The evaluation method makes use of a CAD-CAE integrated program. The model of the bonding module including the bonding tool is constructed in a CAD system and then exported to the finite element analysis software to generate finite element mesh. Through the process of giving the meshed model proper physical properties, boundary conditions and loads, both the structural behaviors of the bonding module and the flatness of the bonding tool can be evaluated. The flatness of the bonding tool can be verified by measuring the contact pressure of the bonding process using pressure indicating films. The experimental result shows that the simulation is almost correct. In conclusion, the result of the evaluation using finite element analysis is close to the responses of the real product, so the evaluation would be an effective approach to design and modify the structure of the PCB bonding modules.