The invention relates to a method for building a shaft system vibration throw analytical expression of a vertical pumping unit shaft system trajectory, and belongs to the technical field of water turbine generator sets. The method for building the shaft system vibration throw analytical expression of the vertical pumping unit shaft system trajectory comprises the steps that additional external force of a motor rotor and a pump runner is converted into a harmonic excitation function, by defining a motor rotor and pump runner throw ratio function, decoupling of a trajectory equation is achieved,and then the analytical expression of the motor rotor and pump runner vibration trajectory is obtained. The shaft system vibration throw analytical expression built through the method can provide theoretical support for researching the pumping set running stability and pumping unit vibration characteristics and vibration characteristic analysis. Meanwhile, the shaft system vibration throw analytical expression can be applied to business software related to pumping set online monitoring, fault diagnosis and the like.