A reaction wheel assembly(RWA) is the largest disturbance source that can induce high frequency micro-vibration on an optical payload of satellites. To ensure a tight pointing-stability budget of satellites, the RWA disturbance effect on spacecraft should be accurately analyzed and evaluated for whole design phases. For this purpose, the micro-vibration disturbance of RWA should be precisely measured. In the present study, two measurement methods on RWA micro-vibration disturbances are compared and investigated. One is a free run-down speed test and the other is a constant speed test. The micro-vibration data measured by the two methods are analyzed in terms of spectrum characteristics, static and dynamic imbalance values, and root sum square(RSS) values. The analysis results show that both methods can measure very similar results in time and frequency domains and that the free run-down speed method is more adequate in respects to wheel friction modeling, noise rejection of imbalance and RSS peak evaluation.