The measured vibrational responses of the pumping station pipeline in the irrigation site were chosen to confirm the chaotic characteristics of the pumping station pipeline vibration and to determine the vibrational excitation that makes it chaotic. First, the chaotic properties of the pipeline vibration responses were investigated using a saturation correlation dimension and the maximum Lyapunov exponent. The vibration excitation with chaotic features was obtained using an improved variational mode decomposition (IVMD) method to examine the multi-time-scale chaotic characteristics of the pipeline vibration responses. The results show that the vibrational responses of each measuring point of the pipeline under different operating conditions have clear chaotic characteristics, where the chaotic characteristics of the axial points and bifurcated pipe points are relatively strong. The vibration of the operating conditions and measurement points affected by the unit’s operation and flow state change is further complicated. The intrinsic mode function (IMF) produces a low-dimensional chaotic attractor after the IVMD disrupts the vibration response. Still, the vibration excitation of the remaining components on behalf of the units does not have chaotic properties, implying that water pulsation excitation makes the pumping station pipeline vibrations chaotic. The vibration excitation caused by the unit’s operation covers the chaotic characteristics of the pipeline vibration and increases its uncertainty. The outcomes of this study provide a theoretical basis for further exploration of the vibration characteristics of pumping station pipelines, and a new method of chaos analysis is proposed.