The experimental study results show that the system’s nonlinear characteristics, incluing the dynamic responses of the poincare mapping, the bifurcation plots, three-dimensional waterfalls diagrams etc. The effects factors of system experiment are studied and analyzed, including the misalignment and the rub-impact stiffness on system responses. So, the faults characteristics of the misalignment and the rub-impact of the rotation shaft-mechanical seal system on the drainge motor and drainge pump are also gained by the experiment. The dynamic performance of the system show nonlinear characteristics in different working conditions. The rotating shaft-mechanical seal system on the drainge motor and drainge pump can be optimization design and performance prediction based on the studied results of our work. The experiment’s results show that: the multiple frequencies are produced of the rotating shaft-mechanical seal system on drainge motor and drainge pump, and the frequencies of 1-time and 2-time are dominating components under the exciting force effects of misalignment and imbalance. At the fault state of misalignment coupling rub-impact, the multiple frequencies including 2-time, 3-time, 4-time and so on, will be induced under the critical speed. Over the value of the critical speed, will cause the phenomenon of frequency demultiplication and chaos. With rub-impact stiffness value increased, the phenomenon of frequency demultiplication and chaos are induced more frequently; with the degree of misalignment increased, the phenomena of chaos will decrease and the system will tend to be the stable state.