This paper presents an indirect measurement method of free velocities from resiliently mounted machines in situ. First, the dynamic equation of the coupled isolation system is established using impedance synthesis analysis. Second, the effective point mobility is utilized to convert the multi-input and multi-input system to a single-input and single-output system. The relationships between the free velocities and the velocities of mounting points of the machine are analyzed. Accordingly, the measurement method of free velocities is obtained. Finally, the errors and adaptive frequency ranges of this method are analyzed respectively. Besides, the accuracy of the proposed method is proved by a numerical simulation example. The results of a test also verify the theory deduction. This study thus provides theoretical references for the measurement of free velocities in practical engineering.