It is more dangerous for the units sharing the same division pipeline system than those sharing individual system during the load rejection transient for a high water head pumped storage station. A new mathematical model for the load rejection transient in these two units sharing the same division pipeline was proposed using method of internal characteristic (MIC). The transient relationship between the geometric parameters and working parameters was established based on the dynamic equations of the hydraulic machinery. Meanwhile, the calculation of the load rejection transient was accomplished and compared with field experimental data from a pumped storage power station. The relative errors of the maximum rotational speed of the two units between the predicted results and the experimental data were −5.9% and −4.44%, respectively, and the relative errors of the maximum rising of hydraulic pressure were −6.7% and −6.98%, respectively. The results met with the design specification requirements, which indicated that the proposed new MIC could completely predict the load rejection transient in these two units with joint closing law of ball-valve and guide vane, and the corresponding calculated results were acceptable and reliable. The MIC is also applicable to the transient investigation of hydraulic systems with hydraulic machinery.