The long-term effectiveness of a neural electrode is the key factor affecting its clinical application, and the optimal design of the electrode is the fundamental way to solve the problem. To optimize the design of the neural electrode, a series of kinetic analysis on the micromotion at the electrode-brain interface was conducted by finite element simulations based on the method of orthogonal experimental design. The influences of five basic parameters of the neural electrode (tip fillet, wedge angle, electrode thickness, stiffness and surface friction coefficient) and their interaction on the micromotion induced injury of brain tissue were studied, and the degree of impact of each factor and the optimal combination were revealed. The results show that the tip fillet, wedge angle and thickness of electrode have a very significant impact on the brain tissue damage. Taking into account the interaction between the factors, the optimal parameters of the electrode are the fillet of 20 μm, wedge angle of 45°, thickness of 40 μm, Young's modulus of 200 GPa, and friction coefficient of 0.1.