To guarantee stable operation and power quality in the turbine units of a hydropower station, an exact mathematical model was built for a long-distance water diversion-type hydropower station with parallel surge chambers. The dynamic characteristics of the hydro-mechanical system were comprehensively simulated, and stability analysis of small fluctuations in the system was conducted. Based on the rigid model and elastic model for the pipe flow, analysis models were established to describe the dynamic characteristics of the hydro-mechanical system. Combined with numerical analysis of both frequency and the time domain, the effects of different layouts of the water diversion system and elastic models with different orders for the pipe flow on the system’s stability analysis were investigated. An example shows that, instead of the commonly used rigid model, which has application limitations, a three-order or higher-order elastic model should be used for the pipe flow at the long-distance water diversion-type hydropower station to fully demonstrate the system’s vibration characteristics and stability performance.