At present, the treatment of transcranial magnetic therapy instrument is mainly manual, with large time intensity and high cost, which seriously restricts the development of domestic transcranial magnetic industry. For this reason, according to the size of GB 2428—1998“Head-face dimensions of adults”, an intelligent transcranial magnetic six axis mechanical arm was designed, which could replace manual hand-held work. It was characterized by high work intensity and flexible treatment schedule. SolidWorks 3D software was used for the overall modeling of the manipulator. Based on the improved D-H parameter method and the Robotics Toolbox toolbox in MATLAB software, the kinematics model of the manipulator was established, and the forward and inverse kinematics equations of the manipulator were derived and solved. Taking the six axis transcranial magnetic manipulator as the research object, a semi simulation test platform was built to carry out the Monte Carlo workspace simulation and path planning simulation. Bidirectional RRT algorithm was used to generate collision free path points, and polynomial interpolation function was used to fit the generated three treatment tracks. Finally, the curves of the whole path track and the angular displacement, angular velocity, angular acceleration and other relevant motion parameters of each joint with time were output. The results show that the six axis mechanical arm can meet the requirements of high precision, high efficiency, flexibility and smooth operation of transcranial magnetic therapy instrument.