In this study, a variable stiffness friction damper was proposed that effectively suppresses micro-vibration output during the orbit attitude adjustment of the spaceborne flywheel and improves dynamic environment during launch. Depending on the actual load conditions of the spaceborne flywheel in orbit and active launching phases, the harmonic balance method was used to obtain the frequency domain force/absolute displacement transmissibility curve. The transmissibility curve was verified via experimental methods. The experimental results show that the variable stiffness friction damper can provide greater damping at the resonance frequency and control the amplification factor to a smaller range. The measured results agree well with the theoretical solution. The research results show that under the effect of small load on-orbit phase, the variable stiffness friction damper can effectively suppress the micro-vibration of the flywheel output. On ensuring high frequency vibration isolation performance, the peak value of the force transmissibility is approximately 6.5. Under heavy load during the launching phase, the peak value of the absolute displacement transmissibility is approximately 2.3. Notably, the variable stiffness friction damper can simultaneously consider the influence of the change of the flywheel load conditions in different working phases, and significantly inhibit its dynamic response.