Based on experimental modal analysis theory, with the method of force-hammer excitation adopted, a single-input-single-output (SISO) structural modal experiment has been conducted on five-axis linkage water-jet whole machines. Combined with the response signal, an experimental modal analysis system has been established, thus acquiring the low-order inherent frequency, the damping ratio and the mode shapes of the whole machine structure, which are to be verified by the modal assurance criterion. A vibration test analysis shows that the first, second and third vibration modes are the main vibration patterns, with its vibration source to be successfully located and some corresponding measures to be taken so as to achieve the purpose of reducing vibration.