A vehicle-mounted three-dimensional underwater particle image velocimetry (PIV) device is used in a towing tank to measure the velocity distribution of the inlet duct of a waterjet ship model in a self-propulsion test. The following points are shown through a comparison of the influences of the stationary and free states of the ship model on the measured results: (1) during the test, the ship attitude will change, specifically, the ship model will heave and trim, (2) the degree of freedom disturbs the processing of the pixel images enough to distort the subsequent image processing, (3) the stationary state of the ship model is the optimal mode for measuring the velocity distribution using the PIV device, and (4) if the changes must be considered, the man-made heaving and trimming may be pre-applied, and be made a corrected stationary mode. In addition, the momentum effect coefficient and the energy effect coefficient are calculated in a non-uniform inflowing state, and the related factors affecting the two coefficients are analyzed. The test results show that the pumping action of the waterjet creates a transverse vector in the cross-sectional speed, which increases the non-uniformity of the inflow. These results could help to establish the design requirements for a waterjet-propelled ship type.