This paper presents the use of a camera-based 3D motion analysis system for non-contact dynamic testing of a highly flexible spinning vertical shaft. The camera system uses high-resolution CMOS cameras to measure instant geometry of the shaft when visible red digital LED strobes are synchronized to work at a speed between 0.1 to 2000 frames per second. Dynamically deformed geometries are obtained by tracing the three-dimensional instantaneous coordinates of markers adhered to the shaft’s outside surface and triangulation techniques for identifying markers’ coordinates. Numerical simulation and experimental results show that the use of camera-based motion analysis systems is feasible and accurate enough for dynamic experiments. For dynamics characterization, we present the use of the Hilbert-Huang transform (HHT) for time frequency analysis of measured dynamic responses. The results show that the third-mode vibration has a cubic nonlinearity.