Shenzhen’s medium-energy high-repetition-rate X-ray free electron laser (Shenzhen Superconducting Soft X-ray Free Electron Laser, S³FEL) requires 1 MHz high-repetition-rate and high-stability kicker. Transmission line structure kicker is an effective way to achieve high repetition rate. However, the insufficient waveform stability of the transmission line structure kicker limits the application of this type of kicker in large particle accelerators. To solve the above problem, this paper studies the input waveform and circuit structure parameters of the transmission line structure kicker. It analyzes the main factors affecting the stability of kicker’s working waveform using mathematical tools such as Fourier analysis, and reveals the relationship between the harmonic order of kicker ideal waveform and the cut-off frequency of kicker transmission line structure. On this basis, this paper proposes a method to reduce the deviation between the actual waveform and the ideal waveform of kicker. This method can obtain the ideal working waveform of kicker within a certain range by adjusting the input waveform parameters or the cut-off frequency of kicker. To verify the above relationship, this paper uses circuit simulation software to simulate different waveforms and different circuit parameters of kicker. The simulation results verify that the above relationship revealed and confirm the effectiveness of the method mentioned.